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Cluster computing - SLURM jobmanager test fails

April 28, 2021, 1:10 pm
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Hello!!

I am new to CONN and trying to integrate it with my computing cluster - SLURM. I have added the configuration settings for my cluster computing; however, when I go to test the configuration it hangs indefinitely.

The test does run successfully under the following scenarios:
  1. submit sbatch command from terminal with generated shell script $ sbatch .qlog/210427151716257/node.0001210427151716257.sh
  2. in matlab: conn_jobmanager('rexec','.qlog/210427151716257/node.0001210427151716257.mat')
  3. in matlab: system('sbatch .qlog/210427151716257/node.0001210427151716257.sh')

So its perplexing as I understand the 'con jobmanager test' command and / or the test profile button in the gui under HCP Option >> Configuration both in essence execute option 3 above. 

Any ideas why the embedded test does not work while these other intermediate checks do?

Thanks
Amy
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Default CONN preprocessing pipeline

April 28, 2021, 5:53 pm
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Hello, 

Previsouly, I used to perform pre-processing in SPM using the following steps:
- the typical ACPC alignment that one does via the 'Display' button in SPM
- Slice time correction
- Realign (Est & Res)
- Coregister (Estimate)
- Segment
- Normalize (Write)
- Smooth



Now I want to use de default pipeline in CONN and I wish to know if it is necessary to perform the ACPC alignment before I insert the images into CONN?
Considering the previous methodology, I believe that all the remaining steps will be performed by the default pipeline in CONN. Is it okay or should I change something?

Thank you!
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Can CONN calculate SNR of a group of subjects?

April 29, 2021, 1:46 am
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Dear Dr Alonso and CONN experts,
I have two cohorts and wish to compare if their data is homogeneous regarding SNR.
Does CONN provide this information?

Also, does CONN provide the value of MVPA´s performance result, population of test and training?

Thank you for your attention
all best!
Renzo
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RE: MVPA analysis questions

April 30, 2021, 12:36 am
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Hi all,
Thank you for discussing MVPA.
I am still strugling to find 2 informations about it:
1- Where\How can I find the information about how well the did the MVPA classifier perform?
2- Which part of the cohort was used for trainning and which was for testing?

Any info or reference suggestion is highly appreciated.

All best
Renzo
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Seed-to-Voxel result error: Can't open file for writing

April 30, 2021, 12:43 am
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Hi,

Thanks for reading this post. 

I'm using CONN to do gPPI analysis on event-related fMRI data. All procedures processed properly (at least no disrupting error). However, when I want to display the results of one ROI seed region, the following error saying "Can't open file for writing: ...path...\CON_Subject001_compA001_001.nii" appeared and no result could be displayed. I checked the directory, the folder was empty, and I could put and write files in it. The other five ROIs I defined worked well. I don't think there is anything special about this ROI. I have re-did all the procedures, but the same error with the same ROI appeared again. 

ERROR DESCRIPTION:
Error using mat2file
Can't open file for writing:
......path.....\CON_Subject001_compA001_001.nii
Check for write permission or whether the directory exists.
Error in file_array/subsasgn>subfun (line 164)
mat2file(sobj,dat,va{:});
Error in file_array/subsasgn (line 85)
subfun(sobj,double(dat),args{:});
Error in spm_write_plane (line 31)
V.private.dat = subsasgn(V.private.dat,S,dat);
Error in spm_write_vol (line 84)
V = spm_write_plane(V,Y,':');
Error in conn_process (line 4645)
spm_write_vol(a,b);
Error in conn_process (line 60)
case 'results_voxel', [varargout{1:nargout}]=conn_process(16,varargin{:});
Error in conn (line 11497)
conn_process('results_voxel','readsingle','seed-to-voxel');
Error in conn (line 10649)
if state==2, conn gui_results_wholebrain;
CONN20.b
SPM12 + Anatomy DEM FieldMap MEEGtools xjview
Matlab v.2019b
project: CONN20.b

I really appreciate it if you can offer some help!

Thanks,
Kayla
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RE: Unequal RT

April 30, 2021, 1:18 am
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Dear Alfonso,
I have also groups of subjects which rsfMRI was acquired with different TRs.

As the current CONN version offers the option, I inserted the different TRs for each group os subjects.

Is the current CONN version automatically implementing what you suggested here in 2012 or do I need to create a second level covariate lebaling the different TRs?

Thank you very much for your attention
All best!
Renzo
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Error when Denoising ROI data

May 2, 2021, 7:13 pm
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Hi all,

I'm trying to run denoising using the CONN GUI with a set of data that I've preprocessed using fmriprep; however, I continue to run into the same error no matter what I've tried. Any thoughts/recommendations at all would be immensely appreciated (details below).

I've loaded all of my fmriprep preprocessed data into CONN 20b and have set the following denoising parameters:

Regression : White Matter (5P) (5 dimensions; no polynomial expansion; no temporal expansion; non-filtered)
Regression : CSF (5P) (5 dimensions; no polynomial expansion; no temporal expansion; non-filtered)
Regression : realignment (24P) (6 dimensions; add quadratic effects; added first-order derivative; non-filtered)
Regression : Matt_Scrubbing(FD>0.9mm) (47P) (47 dimensions; no polynomial expansion; no temporal expansion; non-filtered)
Order : Simultaneous regression and filtering (Simult)
Detrending : 1
Despiking : 0
Bandpass : [0.009 0.08]

Steps 1-3/6 run fine; however, I'm consistently getting the following error description when it comes to step 4/6 (Denoising ROI data):

ERROR DESCRIPTION:

Error using conn_process (line 1658)
Wrong dimensions
Error in conn_process (line 30)
case {'preprocessing_gui','denoising_gui'}, conn_disp(['CONN: RUNNING DENOISING STEP']); conn_process([1.5,2,6:9],varargin{:});
Error in conn (line 6388)
else conn_process('denoising_gui'); ispending=false;
Error in conn_menumanager (line 121)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN20.b
SPM12 + AAL3 ArtRepair DEM FieldMap MEEGtools TFCE cat12 conn marsbar
Matlab v.2020a
project: CONN20.b
storage: 2069.5Gb available
spm @ C:\Users\mvande66\Desktop\Neuroimaging_Programs\spm12
conn @ C:\Users\mvande66\Desktop\Neuroimaging_Programs\spm12\toolbox\conn
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RE: Slice-timing correction error

May 3, 2021, 8:46 am
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[color=#000000]Dear Carmen,[/color]

[color=#000000]Not sure about this, could you please look in your CONN's project log file (e.g. conn_*/logfile.txt) for the description right before the error message and send me that information? should look something like:[/color]

[color=#000000]Preparing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)Performing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)Duplicate application tag in applications 'BasicIO' and 'BasicIO'.
SPM preprocessing job
(1).spm.temporal.st.scans(1) = /Volumes/ext/NYU/NYU_TRT_session1a/sub05676/func/ulfo.nii,1
(1).spm.temporal.st.scans(2) = /Volumes/ext/NYU/NYU_TRT_session1a/sub05676/func/ulfo.nii,2
(1).spm.temporal.st.scans(196) = /Volumes/ext/NYU/NYU_TRT_session1a/sub05676/func/ulfo.nii,196
(1).spm.temporal.st.scans(197) = /Volumes/ext/NYU/NYU_TRT_session1a/sub05676/func/ulfo.nii,197
(1).spm.temporal.st.tr = 2
(1).spm.temporal.st.nslices = 39
(1).spm.temporal.st.ta = 1.94871794871795
(1).spm.temporal.st.so = [0 1025.64102564103 51.2820512820513 1076.92307692308 102.564102564103 1128.20512820513 153.846153846154 1179.48717948718 205.128205128205 1230.76923076923 256.410256410256 1282.05128205128 307.692307692308 1333.33333333333 358.974358974359 1384.61538461538 410.25641025641 1435.89743589744 461.538461538462 1487.17948717949 512.820512820513 1538.46153846154 564.102564102564 1589.74358974359 615.384615384615 1641.02564102564 666.666666666667 1692.30769230769 717.948717948718 1743.58974358974 769.230769230769 1794.87179487179 820.512820512821 1846.15384615385 871.794871794872 1897.4358974359 923.076923076923 1948.71794871795 974.358974358974]
(1).spm.temporal.st.refslice = 974.358974358974[/color]

[color=#000000]Thanks[/color]
[color=#000000]Alfonso
[/color]
[i]Originally posted by Carmen Neuroimage:[/i][quote]Dear CONN experts, 

I downloaded the version of CONN  (20.b) in Linux, and performed functional analysis. I used the default preprocessing pipeline. 
I choose slice-timing: interleave phillips
When slice-timing correction started , an error ocurred: "item 'reference slice', field 'val': item must be an array of natural numbers."

I tried several times, and also choose: slice-timing interleave bottom-up and I also tried entering my own values, but the same error appears.

I would very much appreciate any help with this. 

thank you in advance,

Best regards, 

Carmen[/quote]
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RE: gPPI and session

May 3, 2021, 9:12 am
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[color=#000000]Hi Maite,[/color]

[color=#000000]You should enter the second session data as different session for each subject, and then in the [i]Setup.Conditions [/i]tab you can simply define session-specific conditions (e.g. instead of just 5 task-conditions, define 10 task-conditions, 5 covering the first session data, and another 5 covering the second session). After running gPPI analyses, in the second-level results tab you will be then able to define contrasts comparing the different task effects across the two sessions, e.g. select conditions [session1_taskA session1_taskB session2_taskA session2_taskB] and enter a between-conditions contrast [-1 1 1 -1] to evaluate the hypothesis (taskAsession2-taskBsession2) > (taskAsession1-taskBsession1)[/color]

[color=#000000]Best[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Maite Aznarez-Sanado:[/i][quote]Good morning:
I am using the CONN toolbox in order to perform some gPPI analyses. I have data from a longitudinal study and I would like to assess whether connectivity analyses change as a function of time. Each subject undergoes a fMRI task with 5 different conditions in two different scanning sessions (which take place two months apart). I would like to perform a gPPI analysis for each scanning session and then compare whether connecitivity maps changed across the different scanning sessions. So my question is: How should I introduce the data from the second scanning session? If I introduce it in a different session for each subject, I cannot differentiate between them in the gPPI analysis. On the other hand, if I create a new subject introducing the data from the second scanning session, I am afraid that this analysis won't take into account that this is a repeated-measure design. Could you help me to solve this issue please?
I highly appreciate your help.
Thanks and best regards,
Maite[/quote]
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RE: Error in second-level results

May 3, 2021, 9:18 am
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[color=#000000]Dear Pavan,[/color]

[color=#000000]Sorry, it is not possible to run voxel-level analyses across multiple subjects unless those subjects are in the same space (e.g. in MNI space). If you have subject-specific ROIs you will be able to run ROI-to-ROI analyses (e.g. RRC) across multiple subjects (even if these subjects are in subject-space) but, since there is no between-subject coregistration for individual voxels, voxel-level analyses (e.g. SBC) would not be very meaningful.[/color]

[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso  [/color]
[i]Originally posted by Pavan Bains:[/i][quote]Dear Alfonso,

I am analysing a dataset of 6 participants (2 young adults, 2 old adults, 2 with Alzheimer's disease). The analysis is in native-space thus has used subject-specific ROIs. I just tried computing the second-level results and received an error, but I'm not quite sure what it means:

'ERROR DESCRIPTION:

Error using spm_check_orientations (line 65)
The orientations etc must be identical for this procedure.

Error in spm_spm (line 323)
spm_check_orientations(VY);

Error in conn_process (line 5008)
SPM=spm_spm(SPM);

Error in conn_process (line 60)
case 'results_voxel', [varargout{1:nargout}]=conn_process(16,varargin{:});

Error in conn (line 11497)
conn_process('results_voxel','readsingle','seed-to-voxel');

Error in conn (line 10649)
if state==2, conn gui_results_wholebrain;
CONN20.b
SPM12 + DAiSS DEM FieldMap MEEGtools
Matlab v.2020b
project: CONN20.b
storage: 3822.3Gb available'

In the command window there was the following:

'** The images do not all have same orientation and/or voxel sizes. **
The function assumes that a voxel in one image corresponds exactly
with the same voxel in another. This is not a safe assumption if
the orientation information in the headers or .mat files says that
the images are oriented differently. Please ensure that you process
all data correctly. For example, you may have realigned the images,
but not actually resliced them to be in voxel-wise alignment. 
Here are the orientation matrices of the image volumes. This list
can be used to determine which file(s) are causing the problem.

[-2 0 0 108; 0 1.8876 -0.661029 -70.6382; 0 0.661029 1.8876 -89.7196] /Volumes/My Passport for Mac/MSc Project/Pilot from 22.03/LC_rsfc_pilot_6sub_v1/results/firstlevel/6sub_v1/BETA_Subject001_Condition001_Source005.nii
[-2 0 0 108; 0 1.99011 -0.19864 -94.0521; 0 0.19864 1.99011 -73.6841] /Volumes/My Passport for Mac/MSc Project/Pilot from 22.03/LC_rsfc_pilot_6sub_v1/results/firstlevel/6sub_v1/BETA_Subject002_Condition001_Source005.nii
[-2 0 0 108; 0 1.96839 -0.354169 -88.8764; 0 0.354169 1.96839 -85.0559] /Volumes/My Passport for Mac/MSc Project/Pilot from 22.03/LC_rsfc_pilot_6sub_v1/results/firstlevel/6sub_v1/BETA_Subject003_Condition001_Source005.nii
[-2 0 0 108; 0 1.98754 -0.222938 -96.8922; 0 0.222938 1.98754 -77.5381] /Volumes/My Passport for Mac/MSc Project/Pilot from 22.03/LC_rsfc_pilot_6sub_v1/results/firstlevel/6sub_v1/BETA_Subject004_Condition001_Source005.nii
[-2 0 0 108; 0 1.85697 -0.742736 -78.8394; 0 0.742736 1.85697 -96.3385] /Volumes/My Passport for Mac/MSc Project/Pilot from 22.03/LC_rsfc_pilot_6sub_v1/results/firstlevel/6sub_v1/BETA_Subject005_Condition001_Source005.nii
[-2 0 0 108; 0 1.91261 -0.584743 -72.2799; 0 0.584743 1.91261 -97.2929] /Volumes/My Passport for Mac/MSc Project/Pilot from 22.03/LC_rsfc_pilot_6sub_v1/results/firstlevel/6sub_v1/BETA_Subject006_Condition001_Source005.nii'

Any help would be greatly appreciated.

Kind Regards,
Pavan[/quote]
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RE: Coherence calculation

May 3, 2021, 9:27 am
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[color=#000000]Hi Bryan,[/color]

[color=#000000]One possible way to do this would be to use the option 'frequency-decomposition' in [i]Setup.Conditions [/i](or define your choice of frequency-bands manually there) to define frequency-specific conditions. After that, regular RRC first-level analyses will output correlation coefficient values between each pair of ROIs within each frequency band (so squaring these values will approximate magnitude-squared coherence metrics)[/color]

[color=#000000]Best[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Bryan Jackson:[/i][quote]Hi,


I preprocessed and analyzed resting-state data within CONN and am now trying to figure out a method of determining the coherence (magnitude-squared coherence) of several of my ROIs. Is there a way of analyzing this within CONN? 

Thanks![/quote]
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RE: Error message - Reference to non-existent field 'X1'.

May 3, 2021, 10:01 am
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[color=#000000]Hi Gucy,[/color]

[color=#000000]If possible check in [i]Setup.Options [/i]whether all four analysis-types are enabled (and if not, enable them and then re-run Setup and Denoising steps to make sure CONN goes though all of the standard steps)[/color]

[color=#000000]Best[/color]
[color=#000000]Alfonso
[/color][i]Originally posted by gucy121:[/i][quote][color=#000000]Hi Alfonso,[/color]

[color=#000000]You are right! The Denoising Step didn't finish, and 3/6 Step (Denoising functional data) was skipped. Also, the 4/7 Step was skipped, and functional data was not imported at the Setup Step. I have imported AAL90 template in Setup, which might be related to this error. Could you kindly give me some suggestions? Thank you so much![/color]

[color=#000000]Best,[/color]
[color=#000000]Gucy[/color]
[i]Originally posted by Alfonso Nieto-Castanon:[/i][quote][color=#000000]Hi Nikolov,[/color]

[color=#000000]I believe this error indicates that the Denoising step has not really finished correctly yet. Please check in your project conn_*/results/preprocessing folder whether files named ROI_Subject*_Condition*.mat exist there, and if not, please try re-running the denoising step (and let me know if any error/warning messages occur during denoising)[/color]

[color=#000000]Best[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by nikolov:[/i][quote]+1 - also getting this error consistently when attempting to do rsfmri connectivity analyses with a imported atlas - any insight would be appreciated! 

ERROR DESCRIPTION:

Reference to non-existent field 'X1'.
Error in conn (line 7347)
[CONN_h.menus.m_analyses.X,CONN_h.menus.m_analyses.select,names]=conn_designmatrix(CONN_x.Analyses(ianalysis).regressors,CONN_h.menus.m_analyses.X1,[],{nregressors,nview});
Error in conn (line 6401)
conn gui_analyses;
Error in conn (line 6639)
conn('gui_analysesgo',1);
CONN20.b
SPM12 + DEM FieldMap MEEGtools
Matlab v.2020b
project: CONN20.b
storage: 939.2Gb available[/quote][/quote][/quote]
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RE: how to add realignment parameters in denoising part in conn

May 3, 2021, 10:03 am
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[color=#000000]Hi Anna,[/color]

[color=#000000]Simply enter your rp_*.txt files in CONN's [i]Setup.Covariates (1st-level[/i]) tab as a new "realignment" covariate. After running [i]Setup, [/i]those covariates will show up by default as part of the list of potential confounder effects in the [i]Denoising [/i]tab[/color]

[color=#000000][i] [/i]Best[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by anna_jia:[/i][quote]I 've just start using conn and have tried my best to find a solution to this question, and I was wondering if someone could help me figure out.
I am analysising the task fmri data. I have done the preprocessing in SPM and import the 1st level analysis results in conn.But when doing the denoising,i found the confound list didn't contain realignment,and i wonder how to add realignment parameters in denoising part.
Thank you very much for a reply![/quote]
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RE: CONN batch scripting: How to skip already-done things?

May 3, 2021, 10:27 am
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[color=#000000]Hi Karl,[/color]

[color=#000000]The options are batch.Setup.overwrite, batch.Denoising.overwrite, and batch.Analysis.overwrite (set those fields to 0 when running the Setup, Denoising, or first-level analysis steps, respectively, in order to skip already-processed subject/ROIs; see all conn_batch field details in https://web.conn-toolbox.org/resources/conn_batch)[/color]

[color=#000000]Best[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Karl Lerud:[/i][quote]Could I bump this? My question is basically just how to skip already-processed subjects/ROIs in a CONN batch script. Thanks,

Karl[/quote]
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RE: problem with import from fmriprep - ICA aroma cleaned files not imported

May 3, 2021, 10:36 am
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[color=#000000]Hi Rotem,[/color]

[color=#000000]The simplest way to do this is to let CONN import the (incorrect) desc-preproc_bold.nii.gz files, and then go to the [i]Setup.Functionals [/i]tab, select the option 'Functional tools. Reassign all functional files simultaneously', and then specify there the alternative filenames that you prefer, e.g. you may use a rule of the form:[/color]

[color=#000000]    - in file name[/color]
[color=#000000]    - [b]find[/b] : [i]desc-preproc_bold[/i][/color]
[color=#000000]    - [b]replace with[/b] : [i]desc-smoothAROMAnonaggr_bold[/i][/color]

Best
Alfonso
[i]Originally posted by Rotem Dan:[/i][quote]Hi,

I have a relatively large dataset (108 participants, 4 tasks) that I preprocessed with fmriprep including ICA aroma, and I want to import it to CONN for further denoising and first-level analyses.
However, when using "new (import) from fmriprep dataset", the functional files that are imported are the ~desc-preproc_bold.nii.gz files
and not the ~desc-smoothAROMAnonaggr_bold.nii.gz ones (i.e. the files after aroma non-aggressive cleaning).

Is there a way to import the ~desc-smoothAROMAnonaggr_bold.nii.gz files when importing the dataset?

Thanks!
Rotem[/quote]
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RE: Cluster computing - SLURM jobmanager test fails

May 3, 2021, 10:46 am
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[color=#000000]Hi Amy,[/color]

[color=#000000]If the submitted jobs run normally and CONN hangs indefinitely the issue is probably in one of the following steps:[/color]

[color=#000000]1) some problem when attempting to check the status of the SLURM queue (perhaps check whether squeue commands can be run normally on your system)[/color]

[color=#000000]2) some problem when attempting to terminate the queued jobs if those do not disappear from the SLURM queue automatically (perhaps check whether scancel commands can be run normally on your system)[/color]

[color=#000000]3) some problem re-loading and merging the results from your project (perhaps check whether there are some unusual settings/permission issues when attempting to copy/overwrite files created by your same user but from a different node)[/color]

[color=#000000]If the issue is in (1) CONN will likely show the status of the jobs as 'pending', if the issue is (2) CONN will likely show their status as 'finishing', while if the issue is in (3) CONN will likely show their status as 'finished'. Let me know if your case matches any of the above (and if not, perhaps a few more details about the messages in the command-window while CONN hangs to see if that helps?)[/color]

[color=#000000]Best[/color]
[color=#000000]Alfonso[/color]

[i]Originally posted by Amy Hegarty:[/i][quote]Hello!!

I am new to CONN and trying to integrate it with my computing cluster - SLURM. I have added the configuration settings for my cluster computing; however, when I go to test the configuration it hangs indefinitely.

The test does run successfully under the following scenarios:
  1. submit sbatch command from terminal with generated shell script $ sbatch .qlog/210427151716257/node.0001210427151716257.sh
  2. in matlab: conn_jobmanager('rexec','.qlog/210427151716257/node.0001210427151716257.mat')
  3. in matlab: system('sbatch .qlog/210427151716257/node.0001210427151716257.sh')

So its perplexing as I understand the 'con jobmanager test' command and / or the test profile button in the gui under HCP Option >> Configuration both in essence execute option 3 above. 

Any ideas why the embedded test does not work while these other intermediate checks do?

Thanks
Amy[/quote]
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ROI-to-ROI Connectivity Line Color / Ball Mismatch?

May 3, 2021, 1:58 pm
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I conducted a ROI-to-ROI regression analysis and noticed in the 2nd level model preview figure that there are some ROI connections that have a positive association with my regressed variable and understandably the ball marker for the associated ROI is red colored. However, in some cases the line connecting the ROIs in the positive association model in the preview figure are blue. What does it mean when the ball marker for the ROI is red, yet the connectivity line color is blue?

Does this mean that the ROIs in question are normally anti-correlated, yet the association between these ROIs and the regressed variable is positive (i.e., performance increases when there is increased connectivity in two ROIs that are normally anti-correlated)? Figure attached to illustrate the line color / ball color mismatch for some connections.
Thanks,
Jeff
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How to Interpret Between Subject + Between Condition Contrast

May 4, 2021, 7:27 am
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Hello CONN team,

I have two groups (1 and 2) and two conditions (A and B). We hypothesize that in a given seed region, group 1 would show a greater activation in condition A relative to condition B, compared to group 2. To test this in CONN, we used the following contrasts, and I would like to make sure they are right to analyze this:

[1 -1 0 0] for between-subjects, corresponding to [Group1 Group2 age sex] covariates
[1 -1] for between conditions, corresponding to [ConditionA ConditionB]
 
In terms of the calculation, I see that CONN is reporting a t-statistic. Based on this, I presume that within a subject, the between-condition difference map is calculated first and used as the subject's first-level image, which is then fed into the group analysis employing a 2 sample t-test. Is this the correct way of interpreting the calculations for this set of contrasts?

Thank you,
Steven
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Change in java messages now causing RAM problems

May 4, 2021, 3:33 pm
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Dear Alfonso,

Hope you're well in these unusual times. I have been getting numerous running java messages after loading an analysis, so much so that it takes up RAM and prevents any processing (with windows opening or closing very slowly). We use a Linux computer with Red Hat Enterprise 5, Matlab 2011b, Conn version 16b. We have not made any changes to the OS or Matlab or Conn versions and were surprised when this started to happen as things ran smoothly before. It's been going on for months. Before this started to happen, we would get running java error messages, but they did not influence processing. When using SPM with Matlab, this disruption hasn't appeared so far.  One of the many messages is "Exception in thread 'AWT-EventQueue-0' java.lang.NullPointerException", but you can see more in the attached jpg. The messages keep coming and don't seem to stop. Just wondering what your thoughts are. Thanks!

All the best,
Mary
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RE: Cerebellum Cut Off after Preprocessing

May 4, 2021, 9:05 pm
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Have you fixed up this issue? 
I have the same problem.
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