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RE: grey matter image loss

October 30, 2021, 12:13 am
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[color=#000000]Hi,[/color]

[color=#000000]Here is also the structural image attached. Thank you![/color]

[i]Originally posted by Candan Yasemin Yazicioglu:[/i][quote]Hi Alfonso,

In one of my subjects the grey matter ROI image is blank (very faint image), even though it has good quality structural image in the setup. You can find images attached. Can you help me with this problem?

Thank you so much!

Best,
Yasemin[/quote]
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RE: Second Level Analysis' Output Files

October 31, 2021, 2:01 am
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Hi Alfonso,
Thank you for your answer.

I have a follow up question; 
What is the difference between the files "spmT_": T-statistics map (univariate analysis, generated by SPM), and "spmF_mv": T/F-statistic map (multivariate analyses, generated by CONN)?

Regards,
Mor
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RE: Can ROIs in the default CONN atlas be divided along the long axis?

October 31, 2021, 6:18 pm
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Thank you, Alfonso.

I downloaded version 21.a by using:[code]git clone https://github.com/alfnie/conn [/code]but i get this after trying the new function:[code]>> conn_createsubroi('/neuroimaging_software/conn_dev/conn/rois/atlas.nii', 'newLeftPreCentral.nii', 5, [1 0 0], 14);
[color=#ff0000]Undefined function or variable 'conn_createsubroi'.[/color][/code]
[color=#000000]I removed the old path to stable conn (20) and added the path to the development version (21) instead. When I asked mathlab about the version, it looks like it is the new one being called.[/color][code][color=#000000]>> conn version[/color][/code][code][color=#000000]ans =[/color][/code][code][color=#000000]<span><span style="white-space: pre;"> </span>'CONN (21.a)'</span>[/color][/code]
am I missing something or did I not install it correctly?

Best,

Luis
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RE: script for extracting first level results

October 31, 2021, 8:59 pm
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Hi Bailey,

check out this tutorial by Raphael Vallat. I think it is what you are looking for. 

https://raphaelvallat.com/conn_plot.html
[i]Originally posted by baileyhg:[/i][quote]Hello,

I was wondering if anyone has a matlab script template that can be used to extract the first level results? Specifically, I ran a number of ROI-ROI analyses (e.g., amygdala-mPFC, ACC-amygdala, etc.), and I'd like to have one csv that includes CONN subject ID, ROI-ROI FC values, and mean motion for all subjects. 

Thank you!

Best,
Bailey[/quote]
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movement/outliers as 2nd level covariates?

November 1, 2021, 3:33 am
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Dear Alfonso, dear all

In my conn project, I used the Outlier detection step in the preprocessing, so the 1-level covariate is included in the denoising. However, I am now wondering if I need to include any 2nd level covariate of movement in the 2nd level analysis to control for movement/outliers. Is this necessary or would it be like a "double"-control of it since it is already included in the denoising step?

I ask this because at the follow-up of my study, the study groups (patients and controls) show a group difference of movement (not at baseline). Do I need to control for this in the 2nd level analysis or is it not needed because of the preprocessing/denoising?

Thank you very much for your help!

Best
Anna
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Disappearing of scroll bar in denoise page

November 1, 2021, 6:36 am
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Dear All,

The scroll bar disappears when I try to change the image orientation. For clarity I attached screenrecord. Please have a look and let me know how to fix this issue.
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Different voxel dimension and FOV

November 1, 2021, 6:45 am
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Dear Experts,

In my project work, all participants structrual MRI scans have a voxel dimensions of 1x1x1 with FOV 256x256x175, but one scane dimension is 0.8x0.8x2 with FOV 288x288x175. Functional MRI demensions for all the scans is same.
Can I include ths scan with other scan or should I exclude it for resting state analysis and also for VBM analysis?
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Error when setting up conditions & a question about modelling the hand (button) response

November 1, 2021, 7:01 am
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Hi all,

I am trying to set up onsets and durations for conditions for one of my sessions (manually, using 'specify blocks/events' in the format with dots: 2.83975 & 4.010116, for example), and when I use version 19 of Conn (I am using Matlab 2019b), I get the following error:

ERROR DESCRIPTION:

Dot indexing is not supported for variables of this type.
Error in conn (line 1505)
state=find([conn_menumanager(CONN_h.menus.m_setup_02a,'state') conn_menumanager(CONN_h.menus.m_setup_02b,'state')],1);
CONN19.c
SPM12 + DEM FieldMap MEEGtools imcalc
Matlab v.2019b
project: CONNundetermined

When I do the same in the 2018b version of Conn, the error is gone.


Another question I have is how do I include left hand/right hand button response into my model as a nuisance regressor?

Thanks a lot for any help!

Best wishes,
Valeria
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Error using load: during pre processing but referring to a Second Level (SBC) analysis

November 1, 2021, 12:48 pm
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Dear CONN experts,
At a given moment after performing several Second Level analysis(LC, RC, GC etc) I got this message when I tried SBC.
Then I reloaded all over again my 120 subjects and still got this problem.
Could anybody shed some light please?

All best
Renzo Torrecuso



ERROR DESCRIPTION:

Error using load
Unable to read file '/data/pt_02419/CONN projects/LZ_snr/results/firstlevel/SBC_01/resultsROI_Subject120_Condition001.mat'. No such file or directory.
Error in conn_process (line 4381)
t=load(filename,'Z','regressors','names','names2','xyz','SE','DOF');
Error in conn_projectmanager (line 205)
conn_process(psteps{n}{:});
Error in conn (line 885)
conn_projectmanager('updateproject',fromgui);
Error in conn_jobmanager>conn_jobmanager_gui/conn_jobmanager_update (line 1438)
conn('load',filename);
Error in conn_jobmanager>conn_jobmanager_gui/conn_jobmanager_update (line 1351)
conn_jobmanager_update('finish');
Error in conn_jobmanager>@(varargin)conn_jobmanager_update('refresh') (line 1261)
handles.timer=timer('name','jobmanager','startdelay',1,'period',10,'executionmode','fixedspacing','taskstoexecute',inf,'busymode','drop','timerfcn',@(varargin)conn_jobmanager_update('refresh'));
Error in timer/timercb (line 30)
feval(val{1}, obj, eventStruct, val{2:end});
Error in timercb (line 13)
timercb(t, varargin{2:end});
Error in conn_jobmanager>conn_jobmanager_gui (line 1272)
waitfor(handles.hfig);
Error in conn_jobmanager (line 467)
info=conn_jobmanager_gui(info,files,filedates,varargin{:});
Error in conn_setup_preproc (line 888)
conn_jobmanager(info);
Error in conn (line 1143)
ok=conn_setup_preproc('',varargin{2:end});
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 + DEM FieldMap MEEGtools
Matlab v.2017b
project: CONN20.b
storage: 4571.3Gb available
spm @ /data/hu_torrecuso/Documents/MATLAB/spm12
conn @ /data/hu_torrecuso/Documents/MATLAB/conn
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Incomplete warp/stretch especially in posterior aspects

November 1, 2021, 1:03 pm
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I have some brains (structural T1 & resting EPIs) that are failing to warp completely to templates. Sometimes the frontal end does not appear to stretch all the way to the frontal aspect of the template, but most commonly it has been the posterior end not warping all the way to the posterior aspect of the template. Often if this happens to one image (i.e. the resting EPI) this also occurs to the structural T1, even though I do normalisation separately for them.

What might cause this? What parameters might be able to be changed to deal with these few brains that are not matching well in CONN? I have attempted reorienting the images to the ACPC as best as I can, and as far as I can tell, that is not the issue.

I can provide images from the QA plots if needed to help.

Thanks!
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grey matter denoising problem

November 2, 2021, 12:09 am
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Hi,

One of my subjects do not show an image after denoising even though it seems perfectly fine before the denosing step (looking at structural data etc). Can you help me with this issue? Attached you can see the subject with no image. I believe it is a problem with denoising so is this step adjustable like preprocessing?

Thank you!

Best,
Yasemin
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conn_jobmanager errors

November 2, 2021, 1:03 am
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Hi all,

I am having multiple errors while submitting jobs locally to my cpu. I keep getting errors about Reference to non-existent field 'variables'. see below. 

[code]ERROR DESCRIPTION:

Reference to non-existent field 'variables'.
Error in conn_updatefolders (line 157)
if ~isempty(CONN_x.Analyses(ianalysis).variables)&&isstruct(CONN_x.Analyses(ianalysis).variables)&&~isfield(CONN_x.Analyses(ianalysis).variables,'fbands'), CONN_x.Analyses(ianalysis).variables.fbands=repmat({1},size(CONN_x.Analyses(ianalysis).variables.names)); end
Error in conn (line 928)
conn_updatefolders;
Error in conn_jobmanager>conn_jobmanager_gui/conn_jobmanager_update (line 1439)
conn save;
Error in conn_jobmanager>conn_jobmanager_gui/conn_jobmanager_update (line 1351)
conn_jobmanager_update('finish');
Error in conn_jobmanager>@(varargin)conn_jobmanager_update('refresh') (line 1302)
if isempty(handles.timer), handles.timer=timer('name','jobmanager','startdelay',1,'period',10,'executionmode','fixedspacing','taskstoexecute',inf,'busymode','drop','timerfcn',@(varargin)conn_jobmanager_update('refresh')); end
Error in timer/timercb (line 34)
feval(val{1}, obj, eventStruct, val{2:end});
Error in timercb (line 24)
timercb(obj(idxIntoTimerObject), varargin{2:end});
Error in conn_jobmanager>conn_jobmanager_gui (line 1272)
waitfor(handles.hfig);
Error in conn_jobmanager (line 467)
info=conn_jobmanager_gui(info,files,filedates,varargin{:});
Error in conn_setup_preproc (line 888)
conn_jobmanager(info);
Error in conn (line 1143)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 121)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN20.b<span id="_plain_text_marker"> </span>[/code]
<span>I am not sure where the problem is or how to fix it. </span>

Best,

Luis
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Brown University - Clinical Neuroimaging Research Postdoctoral Opportunity

November 2, 2021, 8:38 am
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Hello CONN enthusiasts!

Are you a basic scientist looking to transition to clinical neuroscience research?

Brown University's Department of Psychiatry and Human Behavior is seeking an outstanding postdoctoral candidate with a strong background in neuroscience, psychology, or cognitive science to join our Clinical Neuroimaging Research Core.

You will gain exposure to research related to a broad range of psychological disorders, psychiatric illnesses, and treatment modalities. Our growing portfolio includes research centered on suicide and self-harm, impulsivity and sensation seeking, risk taking in youths, and mechanisms of treatment response.

This is a one-to-two year postdoctoral appointment, but Brown's exceptionally collaborative research environment provides a wealth of internal opportunities for pilot funding that can help successful fellows transition to a subsequent faculty appointment, K awards, and/or core leadership roles.

Candidates should have 3+ years of graduate-level or postdoctoral experience in human neuroimaging (e.g., task fMRI, rsfMRI, MRI, diffusion) and working knowledge of a relevant programming language (e.g., Python, MATLAB). A strong background in either computational modeling or systems management is not required, but desirable. 

Interested candidates are encouraged to forward their CV and a cover letter to Jennifer_Barredo@brown.edu. Candidates must be U.S. citizens or have permanent resident status.

Look forward to meeting you!
Jennifer Barredo, PhD
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Results first level - Conditions

November 2, 2021, 11:43 am
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Hi, I have a quick question:

I ran data that had 3 scanning sessions (baseline, week 6 and week 16) and some of these subjects have missing data since some did not finish a particular scan, e.g., some subjects may have only one scan or two scans.

When I went to check for the connectivity maps under project/results/first_level/SBC_01, I found that ALL subjects have connectivity maps for all sessions (e.g., BETA_Subject002_Condition001_Source136, BETA_Subject002_Condition002_Source136, and BETA_Subject002_Condition003_Source136). I picked this subject because I know this one only had 1 scan (baseline). I don't understand what CONN did to do this.

Also, some subjects may have 2 scans, but it could be baseline and week6, OR baseline and week16, 0R week6 and week16. The same with subjects who have only one scan.....it could be any of the scanning sessions, but CONN calls the Condition001-003 and they all have data.

I want to import these maps and run linear mixed models outside of CONN, but before I do that, I need to know what CONN did first.

Best,
Omar
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How To Rerun Properly or Preprocess Again After Changing Input?

November 2, 2021, 1:12 pm
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One of my subjects had issues with the skull being included in normalisation. I skull stripped it, and then wanted to select that new skullstripped version and rerun the preprocessing for it. I am not sure of the best way to go about this, and I keep running into errors with QA afterwards.

One method I tried: Select Secondary dataset (original) and import/change input to new skullstripped one. Run preprocessing again for this subject. Update primary dataset for this subject to be the swauo file from this skull stripped. Also, make sure structural is wc0co version. 

Another method: Use primary dataset --> reselect primary dataset functional to be the skullstripped version (not processed) and rerun preprocessing for primary dataset for this subject.

Both methods appear to maybe work? But I get errors in QA looking for a wc0cowc0cowc0co file for my structural, even when I try to change the structural back to the single wc0co structural.

I checked the folders for these subjects and I can see those that I have tried to rerun have a lot of actual files that do not make sense to me, such as the wc0cowc0cowc0co or swauo_swuao files. Clearly, some method I have tried made files that have already been processed be processed again.... I tried to search through for these files and delete this to see if that would help but it didn't.

So I am stuck accidentally processing already processed data, and unsure how to best rerun preprocessing when I want to change the original inputs as I am afraid of messing things up more.

Thanks for the guidance!
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RE: script for extracting first level results

November 2, 2021, 7:37 pm
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Thanks for sharing Luis! That tutorial describes how to extract second level results; I'm wondering if you (or anyone else) can point me to a script for extracting the data from first level analyses?
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RE: Different p-FDR in REX results vs extended stats

November 3, 2021, 5:10 am
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[color=#000000]Hello,[/color]

[color=#000000]I would greatly appreciate it if someone could please help me with answering the question below.[/color]

[color=#000000]Best,[/color]
[color=#000000]N[/color]
[i]Originally posted by Nancy P:[/i][quote]Hello,

There is a discrepancy between p-FDR (but not p-unc) values when I use REX interface to look effect sizes to look at the dynamic ICA results vs when I look at them by checking "display extended stats". Why is there a difference between the two? 

Thanks,
Nancy[/quote]
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first level analysis pre post design

November 3, 2021, 7:38 am
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Hello,

i gently ask some help. i have a design with 8 subjects with 4 sessions each: 2runs for pre and 2 for post
Every subjects and conditions have data, however when i try to run first level analysis (press done after denoising), i receive an error.

Just to describe what i did
1)first i have analyzed only the post (so 2 conditions fo subject).
2) After to have reached the second level analysis, i came back to the setting tab and added the 2 runs for pre.
3)In the condition tab i defined which session was for pre and which for post.
4)Preprocessing and denoise run smootly, while at first level, i received the following error (i use the not overwrite option for every step on the 2 new sessions)


Error using reshape
Number of elements must not change. Use [] as one of the size inputs to automatically calculate the appropriate size for that dimension.

thx
elena
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RE: Can ROIs in the default CONN atlas be divided along the long axis?

November 3, 2021, 11:05 am
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Hi Alfonso,

I am sorry to bug you again with this request. 

I am not sure if the conn_createsubroi function exist in the development  version.

BEst,

Luis

[i]Originally posted by Luis Alvarado:[/i][quote]Thank you, Alfonso.

I downloaded version 21.a by using:[code]git clone https://github.com/alfnie/conn [/code]but i get this after trying the new function:[code]>> conn_createsubroi('/neuroimaging_software/conn_dev/conn/rois/atlas.nii', 'newLeftPreCentral.nii', 5, [1 0 0], 14);
[color=#ff0000]Undefined function or variable 'conn_createsubroi'.[/color][/code]
[color=#000000]I removed the old path to stable conn (20) and added the path to the development version (21) instead. When I asked mathlab about the version, it looks like it is the new one being called.[/color][code][color=#000000]>> conn version[/color][/code][code][color=#000000]ans =[/color][/code][code][color=#000000]<span><span style="white-space: pre;"> </span>'CONN (21.a)'</span>[/color][/code]
am I missing something or did I not install it correctly?

Best,

Luis[/quote]
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importing from fmriprep - issue with MNI space

November 3, 2021, 12:09 pm
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Hi all,

This is not an issue with CONN - just something we recently noticed and I was wondering if others saw that, too.
When we import data after they had been fmriprep-ed in one of the recent versions, we expect the data to all be in the same space (MNI).
However, when looking at the EPI data in CONN, subject by subject, there are clearly some alignment/normalization issues, such that the subjects are kind of in MNI space, but not exactly, with some minor differences between subjects. This was not the case with older fmriprep versions (maybe up to 6 months ago), but we have now seen it multiple times with different datasets in newer versions.
Again, this is probably not a CONN issue, but rather a bug in fmriprep (might be related to field maps; they don't really say). CONN just allows us to notice those subtle differences since the interface enables us to quickly go subject by subject.

I'm just wondering if anyone else has experienced this when importing fmriprep data.

Thanks,
Rany
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