Freesurfer March 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
172 discussions

PETSurfer: Equivalence between surfaces un gtmseg space and native surface?
by Matthieu Vanhoutte 07 Mar '19

07 Mar '19

External Email - Use Caution Dear Douglas, RBV PVC use the advantage of upsampled gtmseg space at 0.5 mm3 to compute PVCorrected images. Would it be beneficial to project this PVCorrected images onto gtmseg space surfaces to keep this upsampled resolution ? Or would it be equivalent to project these PVCorrected images on gtmseg space onto native surfaces using --reg rbv2anat.lta ? Best, Matthieu

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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

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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>

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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

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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

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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

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Cerebellar Cortex Reconstruction
by Max Crayen 06 Mar '19

06 Mar '19

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Freesurfer March 2019