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. <dgr...@mgh.harvard.edu> Sent: Thursday, January 2, 2020 11:46 AM To: Nasiriavanaki, Zahra <znasiriavan...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Thursday, January 2, 2020 10:57 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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