The easiest thing to do is to probably do the concatenation by hand, eg,
mri_concat subj/sess01/analysis/contrast/ces.nii.gz subj/sess01/analysis/contrast/ces.nii.gz --o ces.sess01+sess02.nii.gz
mri_concat subj/sess01/analysis/contrast/cesvar.nii.gz subj/sess01/analysis/contrast/cesvar.nii.gz --o cesvar.sess01+sess02.nii.gz

Create a dof file by adding together the dofs for each individual analysis as indicated by these values. Just put this number into a text file, eg, dof.sess01+sess02.dat
cat subj/sess01/analysis/dof.dat subj/sess01/analysis/dof.dat

Create a mask
fscalc subj/sess01/analysis/mask.nii.gz and subj/sess01/analysis/mask.nii.gz -o mask.sess01+sess02.nii.gz

Then run glmfit like
mri_glmfit --surface subject lh --y ces.sess01+sess02.nii.gz --yffxvar cesvar.sess01+sess02.nii.gz --ffxdofdat dof.sess01+sess02.dat --mask mask.sess01+sess02.nii.gz --osgm --o ffx/subject/analysis/contrast/osgm

On 1/2/2020 11:20 AM, Nasiriavanaki, Zahra wrote:

I want to concatenate the two sessions which I guess is the same as combining them statistically.

Please note that it's all done in "self" space not fsaverage.

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129

From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Thursday, January 2, 2020 11:46 AM
To: Nasiriavanaki, Zahra <ZNASIRIAVANAKI@mgh.harvard.edu>; freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] highres fMRI selxavg error
When you say you need to see them together, what does that mean? Are you computing contrasts between the two sessions or you just want to combine them statistically?

On 1/2/2020 10:07 AM, Nasiriavanaki, Zahra wrote:
I need to concatenate the two sessions. We scanned the subjects twice with the same task.

I need to see the maps for each session separately and also together.

Thanks

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Thursday, January 2, 2020 10:57 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] highres fMRI selxavg error
Why are you combining them into one bold folder?

On 12/30/2019 9:09 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurfer experts

Happy Holidays!

I have a subject with two highres fMRI scan sessions. Attached you can see an image, showing how I organized the sub-folders.

I preprocessed the bold1 and bold2 and then copied the preprocessed files to "bold from both sessions" folder. I ran selxavg for bold1 and bold2 seperately and it went well.

However, when I ran selxavg for "bold from both sessions" folder, it gives the below error.

Could you please let me know what the problem is?Also if you have a better suggestion for how I should organize my subfolders/analysis, I appreciate that.

Thanks

Mona

>> >> >> >> /autofs/cluster/freesurfer/centos7_x86_64/stable6/fsfast/toolbox/fast_selxavg3.m

>> /autofs/cluster/freesurfer/centos7_x86_64/stable6/fsfast/toolbox/fast_ldanaflac.m

>> /autofs/cluster/freesurfer/centos7_x86_64/stable6/matlab/MRIread.m

>> >> >> starting fast_selxavg3b

#@# arap_7T_all ###############################

/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all

-------------------------

$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $

-------------------------

outtop = /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects

Extension format = nii.gz

INFO: key nSliceGroups unrecognized, line 12, skipping

1 app.mat

2 aw.mat

3 caw.mat

4 clo.mat

5 faw.mat

6 fem.mat

7 fm.mat

8 fmaw.mat

9 mal.mat

10 maw.mat

11 oaw.mat

12 oc.mat

13 ocaw.mat

14 ope.mat

15 wit.mat

Excluding 6 points

nruns = 15

autostimdur =

outanadir = /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all/loom/loom_native.lh

Excluding 6 points

Excluding 0 points

Excluding 1 points

Excluding 5 points

Excluding 8 points

Excluding 3 points

Excluding 8 points

Excluding 4 points

Excluding 6 points

Excluding 10 points

Excluding 5 points

Excluding 5 points

Excluding 5 points

Excluding 5 points

Excluding 5 points

parfiles condition id list: 1 2 3 4 5 6 7 8

Found 41883/148565 (28.2) voxels in mask 1

Creating Design Matrix

... creation time = 0.040 sec

DoMCFit = 1

ntptot = 1350, nX = 219, DOF = 1131

Saving X matrix to /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all/loom/loom_native.lh/Xtmp.mat

XCond = 1873.07 (normalized)

Computing compensation for resdual AR1 bias

1 -0.5 -0.456169 (t=1.17104)

2 -0.25 -0.261165 (t=2.14097)

3 0 -0.076309 (t=2.3701)

4 0.25 0.0914527 (t=3.32529)

5 0.5 0.225506 (t=4.09175)

AR1 Correction M: 0.138222 1.44983

Computing contrast matrices

Computing contrasts

Loading previous GLM fit

Starting contrasts

app J=1 -------------

Error using *

Incorrect dimensions for matrix multiplication. Check that the number of

columns in the first matrix matches the number of rows in the second matrix. To

perform element wise multiplication, use '.*'.

Error in fast_fratiow (line 81)

ces = C*beta;

Error in fast_selxavg3b (line 1153)

fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:));

>> ------------------------------------------

ERROR: fast_selxavg3() failed\n

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129
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