Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Creating Labels
by Jahan, Bushra 07 Mar '19

07 Mar '19

Hello, I am wondering how to generate a label in FreeSurfer from peak activation in a cluster - is there a specific command? Thank you.

2 1

Re: [Freesurfer] Resampling a gifti image to nifti using mri_surf2vol fails
by CAGNA Bastien 07 Mar '19

07 Mar '19

External Email - Use Caution Hi, First I tried to use my original mask which is a gifti with a single darray as NIFTI_INTENT_ESTIMATE that contains 0 or 1 for each vertex. But I got it: " ** DA[0] has coordsys with intent NIFTI_INTENT_ESTIMATE (should be NIFTI_INTENT_POINTSET) MRISreadGiftiAsMRI: no overlay data found in file [filename] " So I changed darray to a new one that contains only the list of the point coordinates where my mask is equal to 1 (and use NIFTI_INTENT_POINTSET) and now I have only this error: " MRISreadGiftiAsMRI: no overlay data found in file [filename] " Bastien

2 1

unable to map surface to fsaverage4
by Chenfei YE 07 Mar '19

07 Mar '19

External Email - Use Caution Hi, I'm following the process described in https://www.cloudneuro.org/ to predict age based on cortical thickness of an individual brain. I cannot map surface to the fsaverage4 template by the 2nd command: recon-all -s subject.id -qcache -target fsaverage4The error was shown like mri_surf2surf: could not read surface ./test2/surf/lh.fsaverage4.sphere.regNo such file or directory I tried to change the 1st command like: recon-all -i input_image -s subject.id -all -target fsavearge4But still the same error. My FreeSurfer version is 6.0.0. Maybe that's why I cannot successfully run the code in https://www.cloudneuro.org/. But is there any way to solve this problem? Thank you. Chenfei

3 4

PETSurfer and thickness data
by Boris Rauchmann 06 Mar '19

06 Mar '19

External Email - Use Caution Dear FS community, I would like to assess how PET tracer uptake is related to thickness changes in AD patients. Is it possible to generate difference maps for both methods and run a GLM? Or would you suggest another approach? Thanks, Boris

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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08
by Arsenije Subotic 06 Mar '19

06 Mar '19

External Email - Use Caution Hi, I am still struggling to examine differences in thickness using the command line stream for my two groups after controlling for age and sex. I get the following error when running the command line: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd CAA_CTRL_RH_Age_Sex.fsgd --C Contrasts/CAA-CTRL_Age_Sex.mtx --surf fsaverage rh --cortex --glmdir CAA_CTRL_RH_Age_Sex_Unix.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.000000 (col 5), Max=611.699463 (col 4) The scale is much different between columns 5 and 4, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 5, all values are 0 Column 6, all values are 0 Columns 5 and 6 are the same My design matrix is: 1 -1 0 0 0 0 (Examining difference in thickness after controlling for effects of age and sex) Iâ€™ve also attached the FSGD file that Iâ€™ve been using. Please let me know if there is something wrong with the file (although I have used a similar file without the covariates and did not have any issues). Thanks! Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca<mailto:arsenije.subotic1@ucalgary.ca>

2 1

Masks in mri_segstats
by Zhi Li 06 Mar '19

06 Mar '19

External Email - Use Caution Hello Freesurfer experts, I would like to use mri_segstats with two different masks and thresholds, such as: mri_segstats --mask mask1 --maskthresh thresh1 --mask mask2 --maskthresh thresh2 This command can run smoothly with our any error. However, I am not clear if the results are correct. I mean if mri_segstats uses the overlap between two masks or only uses the last input mask and threshold? Any suggestions? Thank you and best regards, Lizhi

2 1

How to extract cortical features of a ROI
by 310913949 06 Mar '19

06 Mar '19

External Email - Use Caution Dear Freesurfer Experts, I want to extract cortical features of a ROI that I drawn manually on the rawavg.mgz in Freesurfer, but i don't know how to do that. I think maybe first the lesion mask should be registered to the standard templates fsaverage, but I don't know what the command line is , could you tell me? And secondly, I should use mri_label2label to map the label to individual subject and extract the cortical features of the ROI, am I right? I am looking forward to your reply!Thanks. Best wishes! Kan Deng

3 4

Resampling a gifti image to nifti using mri_surf2vol fails
by CAGNA Bastien 06 Mar '19

06 Mar '19

External Email - Use Caution Hi everyone, I need to convert a surfacic mask that is made from data of one subject projected onto fsaverage6 into a volumic map. To do so, I'm trying to use mri_surf2vol to take my Gifti file and create 3D version as Nifti file (using gray matter). So, I tryed this: mri_surf2vol --sd [subjects_dir] --subject fsaverage6 --o [output_filename].nii.gz --so [subjects_dir]/fsaverage6/surf/lh.white [lh.surf_mask_filename].gii --so [subjects_dir]/fsaverage6/surf/lh.white [rh.surf_mask_filename].gii But it failed and tells me: MRISreadGiftiAsMRI: no overlay data found in file [lh.surf_mask_filename].gii After quickly looking to the source code, at line 1077 of utils/gifti.cpp: /*----------------------------------------------------------- MRISreadGiftiAsMRI() - reads GIFTI functional frames into an MRI volume struct, which is a retro-fit usage to store multiple frames of data (where in this case, a frame is one complete vector of vertices). This routine will only read NIFTI_INTENT_TIME_SERIES data arrays. -----------------------------------------------------------*/ I'm getting confused because (from what I understood) this function is trying to read gifti's data in a nifti and moreover i didn't find any example on the web of resampling Gifti file to Nifti image using mri_surf2vol. I think I missing some think but do not understand what. Does any one have an idea about it? Best regards, Bastien CAGNA

2 1

Cerebellar Cortex Reconstruction
by Max Crayen 06 Mar '19

06 Mar '19

3 3

recon-all Workflow Help
by Riya Chatterjee 06 Mar '19

06 Mar '19

External Email - Use Caution Hi, I am new to FreeSurfer - I am a high school sophomore trying to learn more about processing brain MRI's. I have read through most of the documentation, but I was not sure about the workflow for processing an MRI. I am trying to extract just surfaces and was wondering if I can run "recon-all -autorecon2 -pial..." without running "recon-all -all...". Basically, I'm trying to see if I need to run the "recon-all -all..." step before running any of the sub-processes. I would greatly appreciate any advice I could get on this, thanks. Thanks, Riya C

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