Thanks Doug. However, I am running freesurfer analysis on my personal computer and I don't have matlab. Also, I don't know how this matlab script works/ matlab works. Any instructions on how to use it or alternate? Please and thank you. Best, Paul.
On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
It is a table of data, so you can't visualize it directly on anything. You can try using annotval2surfoverlay.m to create a surface overlay of the data.
On 04/19/2017 10:05 AM, miracle ozzoude wrote:
Hello Doug, It worked. The issue was due to formatting error with the aparc file. Also, I was trying to visualize the result on the surface using freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on freeview and loading the sig.mgh). However, i got an error " failed to display overlay". How can I visualize the result? Thanks Best, Paul
On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You have a table of data, so no template is needed. If you put the --surf before the --table, it probably runs, but it will ignore the surface On 4/18/17 9:58 PM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> wrote:Thanks doug. Does it mean when using the --table flag, you can't use the fsaverage template? I came across several post in the forum that used "--surf fsaverage lh " and it worked. Best, Paul Sent from my BlackBerry 10 smartphone. *From: *Douglas Greve *Sent: *Tuesday, April 18, 2017 9:52 PM *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Reply To: *Freesurfer support list *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag Don't include --surf fsaverage lh. It thinks the input is a surface, not a table On 4/18/17 9:21 PM, miracle ozzoude wrote:Hello freesurfer, I am trying to run mri_glmfit with the --table flag. My aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness values for 32 subjects. I ran the glm command and received an error. Please, how can i solve this issue? I have included my command, fsgd file, contrast matrix and error below. Thanks Best, Paul GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir ERROR= "gdfRead(): reading age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 39.9375 17.3312 Class Means of each Continuous Variable 1 Group1 35.6316 2 Group2 46.2308 INFO: gd2mtx_method is dods Reading source surface /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Users/MiracleOz/Documents/improvervsdeclinermri cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir sysname Darwin hostname MacBook-Pro.local machine x86_64 user MiracleOz FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
logyflag 0 usedti 0 FSGD age.fsgd labelmask /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
maskinv 0 glmdir lh.thickness.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.thickness.glmdir Loading y from /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
Found 66 data colums Found 0 data rows INFO: gd2mtx_method is dods Saving design matrix to lh.thickness.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 32.2165 Matrix condition is 20734.7 Found 149955 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 163842, nv1 = 66 search space = 82219.962936 ERROR: dimension mismatch between y and X. y has 0 inputs, X has 32 rows." FSGD file: GroupDescriptorFile 1 Title MOT Class Group1 Class Group2 Variables Age Input 01053p Group1 23 Input 01054p Group1 43 Input 01061p Group2 39 Input 01062p Group2 19 Input 01074p Group2 28 .............. (I have more participants) CONTRAST MATRIX: 1 -1 0 0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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