Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

FreeSurfer Course Registration now open!
by Allison Stevens 02 Aug '16

02 Aug '16

The Freesurfer group is offering a four-day Freesurfer Tutorial and Workshop September 26th to 29th, 2016 at the Martinos Center in Charlestown, MA. You can register for the course on our course website: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Details about the content of the course, the location, registration fees, accepted payment types, and nearby hotels is currently on the website above. Please read the above page in its entirety before registering and before sending questions. If you are not one of the first 50 to register, you will be put on a waiting list and will be notified if a spot becomes available. *Do not submit a payment or make travel arrangements until you have received an email confirmation that you successfully secured a seat in the course. Allison Stevens > Lab Manager > FreeSurfer Development Team > Laboratory for Computational Neuroimaging > Massachusetts General Hospital > Athinoula A. Martinos Center for Biomedical Imaging > Bldg. 149, 13th Street, CNY 2301 > Charlestown, MA 02129

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Re: [Freesurfer] brain mask and T1 are not the same size
by Isabelle Deschamps 01 Aug '16

01 Aug '16

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Where are time series from adjusted (post selxavg3) ROIs
by ERIK JAHNER 01 Aug '16

01 Aug '16

Dear Freesurfer experts I have been going through the documentation trying to figure out how to extract the time series for an ROI (Posteriorcingulate) after removing the regressors that I put in my mkanalysis-sess. I have run the selxavg3. 1. Is this time course what is in the meanfunc.nii.gz? 2. If it is, how do I pull this out in matrix format (.mat) out of the where I basically get one mean adjusted value for the ROI at each timepoint? (e.g. For the Posteriorcingulate, I want 210 values representing the mean activation after removing the effect of my covariates wm and css for each of the 210 timepoints). 3. Is this information in the X.mat file? If so, what is its location? Thanks Erik Jahner

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Running Retinotopy in FSFAST, Design Matrix has Empty Regressors
by Taylor, Johnmark 01 Aug '16

01 Aug '16

Hello, I am trying to run a retinotopy analysis in fsfast, using only polar angle. However, when I try to run it, I am getting the error "Input to SVD must not contain NaN or Inf." I have traced this error and it looks like the design matrix X has 12 regressors (the first 12) that consist solely of zeros. I am using the following commands: mkanalysis-sess -analysis retinotopy -fsd bold -runlistfile runlist.txt -native -funcstem fmc -nuisreg mcextreg 3 -retinotopy 36.4 -per-session -paradigm retino.par -inorm -spmhrf 0 -TR .650 -polyfit 2 -nskip 19 selxavg3-sess -analysis retinotopy -sf sublist.txt -df sessdir Any idea what the first 12 regressors in the design matrix might correspond to in retinotopy analyses and why they'd be empty? I have looked at the documentation and there doesn't seem to be a clear labeling of the retinotopy design matrix anywhere, although perhaps I'm missing something. Thank you very much, JohnMark

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Fwd: question about volume of mask
by Dorsa Haji Ghaffari 01 Aug '16

01 Aug '16

Hi Bruce, I was able to reslice the thalamus mask correctly, but when I measure the volume of the resliced thalamus, is not the same as the original thalamus. I was wondering why that is happening and which volume is more accurate. I appreciate any suggestions. I have attached both masks. Also can you tell me how to measure the volume of the resliced thalamus in Freesurfer? Thank you Dorsa

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ALE map to surface
by Carla Ammons 01 Aug '16

01 Aug '16

Hi! I am new to freesurfer so this may be a basic question. I have an activation map (.nii) created via ALE meta-analysis in MNI space that I want to visualize on the surface. Do I use bbregister for this? Thanks! Carla

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Creating contrast between two groups, controlling for 2 categorical(gender, scanner) and one continous variable(age)
by Oana Georgiana Rus 01 Aug '16

01 Aug '16

Dear FreeSurfer Experts, I want to compare structural measures(eg. thickness) between patients and controls controling for the effects of age, gender and scanner (parts of sample were scanned in scanner 1 parts in scanner 2). I want to answer the question: *do patients and controls differ significantly in lGI when controlling for age (continous variable), gender(male/female), scanner(scanner1/scanner2)?* *so i have to categorical (gender, scanner) and one continous variable to control for.* *my FSGD file looks like:* /GroupDescriptorFile 1 // //Class PatientFemaleScanner1// //Class PatientFemaleScanner2// //Class PatientMaleScanner1// //Class PatientMaleScanner2// //Class ControlFemaleScanner1// //Class ControlFemaleScanner2// //Class ControlMaleScanner1// //Class ControlMaleScanner2// //Variables Age // //Input subject1 ControlMaleScanner1 23.6// //Input subject2 ControlFemaleScanner2 37.7// //Input subject3 PatientFemaleScanner1 32.6/ ... *Total I would have 16 regressors with following contrasts: * *first conrast:* is there a difference in structural measure(eg. thickness) between *patients and controls* controlling for gender, scanner, age? 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 *second contrast:* is there a difference between the two scanners *scanner 1 and 2* controlling for effects of gender, age and group? 0.25 -0.25 0.25 -0.25 0.25 -0.25 0.25 -0.25 0 0 0 0 0 0 0 0 *Questions:* * Are the Contrasts created ok? * How could I control better for the effect of scanner, as part of the sample was scanned with scanner 1 another part with scanner 2? Thank you very much for your help! Geo -- Oana Georgiana Rus PhD Student Neuroimaging Center TUM-NIC Klinikum rechts der Isar Technische Universität München Einsteinstr.1 81675 München Raum 5.8 Tel. 089 4140 7971

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MNI coordinates of all the vertices of fsaverage
by Sabin Khadka 01 Aug '16

01 Aug '16

Hi Doug, I tried to pick up from the thread below to get MNI coordinates of each destrieux parcellation region. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html I created label files from mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation aparc.a2009s --outdir label_destrieux # which works fine And I tried to get the coordinates of each labels using mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel <label file> --sum <output file> --centroid --thmin 0 --hemi lh --subject fsaverage But, all left labels would produce the same coordinates and so does right labels. (I've attached few example files here with). Also, it says TalX, TalY, TalZ are these coordinates in MNI or Talairach? Thanks for help.

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Long seg for hippo subfields
by Thomas, Adam (NIH/NIMH) [E] 01 Aug '16

01 Aug '16

This look very cool: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields But the flag is not being recognized by recon-all using the most recent build: [adamt@felix scratch]$ cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos6_x86_64-dev-20160730-bda65ec [adamt@felix scratch]$ recon-all -long-hippocampal-subfields-T1 md105Templ -hsfTP md105-1.long.md105Templ -hsfTP md105-2.long.md105Templ -hsfTP md105-3.long.md105Templ -hsfTP md105-4.long.md105Temp1 -hsfTP md105-5.long.md105Templ ERROR: Flag -long-hippocampal-subfields-T1 unrecognized. -long-hippocampal-subfields-T1 md105Templ -hsfTP md105-1.long.md105Templ -hsfTP md105-2.long.md105Templ -hsfTP md105-3.long.md105Templ -hsfTP md105-4.long.md105Temp1 -hsfTP md105-5.long.md105Templ Linux felix.nimh.nih.gov 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Mon Aug 1 18:42:51 EDT 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [adamt@felix scratch]$ uname -a Linux felix.nimh.nih.gov 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux [adamt@felix scratch]$ which recon-all /data/adamt/Apps/fs6-2016-07-31/bin/recon-all [adamt@felix scratch]$ Is there a newer version of recon-all hiding somewhere? Thanks, -Adam

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mris_label2annot
by Caroline Beelen 01 Aug '16

01 Aug '16

Dear FS, Sorry to bother again, but I'm currently in need for some quick help. Today, I also ran into another problem. I tried to display only few ROI's in Freeview instead of the whole brain. Therefore, I tried to create a new annotation file consisting of only few labels (from regions of DK-atlas) and I used the mri_annotation2label on my own created fsaverage to get these labels. This worked fine. Then I used the command of mris_label2annot to create the annotation file, but part of the command, --ctab aparc.annotation.ctab, is not recognized. Replacing it by -ctab fsaverage/label/lh.aparc.annot (file exists in the label folder of fsaverage) gives me the following error: CTABreadASCII: badly formed file. ERROR: reading fsaverage/label/lh.aparc.annot. I couldn't find, or create, any other aparc.annot file. What would be the right command (for the part of ctab) to get mris_label2annot working? Or is there perhaps a better way to only display certain ROI's in Freeview? (the latter I could still explore but assistance is certainly appreciated) Thanks a lot! Caroline

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