Re: [Freesurfer] ERROR: dimension mismatch between X and

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Thank you so much for your help - it's working now.

---------------------------------------- Lea Backhausen Wissenschaftliche Hilfskraft

Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie

Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de

_____________________________________________________________________________________ Date: Thu, 27 Sep 2018 15:24:01 +0000 From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: dimension mismatch between X and contrast To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 09411cf0-185b-26c6-9ad0-479edb2d6e2c@mgh.harvard.edu Content-Type: text/plain; charset="Windows-1252"

You have 3 groups and 2 covariates, so you will have 3*(2+1)=9 regressors, in this order ADHD-offset COM-offset TD-offset ADHD-Age COM-Age TD-AGE ADHC-IQ COM-IQ TD-IQ You will need to have a single value for each regressor in your contrast matrix, meaning that you should have 9 values. You have 10 values, thus the error.

On 09/27/2018 09:39 AM, Backhausen, Lea wrote:

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Dear FreeSurfer experts,

I get this error message when running group analysis on cortical thickness using glmfit: ERROR: dimension mismatch between X and contrast Contrasts/ADHD_COM_TD_age_IQ.mtx X has 9 cols, C has 10 cols

Please find attached the FSGD file, the contrast file and the terminal output below.

I want to do ANCOVA with three groups (ADHD, COM and TD) controlling for the effects of age and IQ. So I assume the regressors would be ADHD COM TD age IQ and my contras matrix 1 -1 0 0 0 1 0 -1 0 0 according to information from these two tutorials: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V and https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V.

Can anybody help me out? Where am I wrong? Why does glmfit assume X has 9 cols?

Any help would be much appreciated, thank you in advance!

Best Lea

Terminal Output: mri_glmfit --y rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx --surf fsaverage rh --cortex --glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir gdfRead(): reading FSGD/ADHD_COM_TD_orig_age_IQ.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 13.6015 1.73148 1 IQ 107.288 11.1649 Class Means of each Continuous Variable 1 ADHD? 13.7193 104.3478 2 COM? 12.8657 105.3929 3 TD? 14.0119 112.3784 INFO: gd2mtx_method is dods Reading source surface /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ SUBJECTS/fsaverage/surf/rh.white Number of vertices 163842 Number of faces??? 327680 Total area???????? 65020.839844 AvgVtxArea?????? 0.396851 AvgVtxDist?????? 0.717994 StdVtxDist?????? 0.193566

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ SUBJECTS cmdline mri_glmfit.bin --y rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx --surf fsaverage rh --cortex --glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir sysname? Darwin hostname edr06188.dip.tu-dresden.de machine? x86_64 user???? Lea FixVertexAreaFlag = 1 UseMaskWithSmoothing???? 1 OneSampleGroupMean 0 y /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh logyflag 0 usedti? 0 FSGD FSGD/ADHD_COM_TD_orig_age_IQ.fsgd labelmask /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ SUBJECTS/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir Loading y from /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh ?? ... done reading. INFO: gd2mtx_method is dods Saving design matrix to rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 1027 Matrix condition is 4.07619e+06 Found 149926 points in label. Pruning voxels by thr: 1.175494e-38 Found 149926 voxels in mask Saving mask to rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74490.844410 ERROR: dimension mismatch between X and contrast Contrasts/ADHD_COM_TD_age_IQ.mtx?????? X has 9 cols, C has 10 cols

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Message: 6 Date: Thu, 27 Sep 2018 15:38:38 +0000 From: "Hoopes, Andrew" AHOOPES@mgh.harvard.edu Subject: Re: [Freesurfer] Best way to update Freeview To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 4CBE100D-0B0E-4B8D-B21B-4520523B668D@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"

Hi Arkadiy, this should be fixed now.

best, Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Maksimovskiy, Arkadiy" AMAKSIMOVSKIY@mclean.harvard.edu Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Wednesday, September 26, 2018 at 6:01 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Best way to update Freeview

Hi everyone,

I was able to download Freeview- the link now works. However I am having an issue with starting this version.

bash-3.2$ export FREESURFER_HOME=/Applications/freesurfer_6.0/

bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

-------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c --------

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME /Applications/freesurfer_6.0/

FSFAST_HOME /Applications/freesurfer_6.0/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR /Volumes/DrEmetBrown/

MNI_DIR /Applications/freesurfer_6.0/mni

bash-3.2$ freeview

dyld: Library not loaded: @rpath/QtWidgets.framework/Versions/5/QtWidgets

Referenced from: /Applications/freesurfer_6.0//Freeview.app/Contents/MacOS/Freeview

Reason: image not found

Abort

I am running a Mac OS HighSierra (10.13.6).

It seems that people had similar issues in the past, but not quiet like this one. I would love to hear any tips on how to fix it.

Thanks, arkadiy

-- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School