Freesurfer

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30070 discussions

Preproc-sess crashed - 3dvolreg.afni error
by Gillian Grennan 09 Nov '22

09 Nov '22

External Email - Use Caution Hello FreeSurfer Developers, I downloaded Freesurfer v7.3.2 <https://secure-web.cisco.com/1VuI2ndzXo5YBm-YeBraBeuWIVo2R7T-txZ30nSNYbmoPI…> onto my local drive and am attempting to run preprocessing through FSFAST. I wasn't able to get access to the .tar.gz Darwin file but downloaded Xquartz, Freesurfer, FSL, and Matlab individually and was able to source Freesurfer using the following commands: export FREESURFER_HOME=/Applications/freesurfer/7.3.2 export PROJECT_DIR=/Users/angelafang/Library/CloudStorage/OneDrive-UW/VicExt export SUBJECTS_DIR=$PROJECT_DIR/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh However, when I run preproc-sess in my analysis folder I get the following error: command: preproc-sess -sf subjectlist -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run error message: ++ Initializing alignment base Choleski factorization failure in startup_lsqfit mri_startup_lsqfit: bad call to startup_lsqfit! ++ Starting final pass on 44 sub-bricks: 0 Fatal Signal 11 (SIGSEGV) received mri_3dalign_one 3dvolreg main Bottom of Debug Stack ** AFNI version = AFNI_2011_12_21_1014 Compile date = May 22 2013 ** [[Precompiled binary macosx_10.7_Intel_64: May 22 2013]] ** Program Abort ** ** If you report this crash to the AFNI message board, ** please copy the error messages EXACTLY, and give ** the command line you used to run the program, and ** any other information needed to repeat the problem. ** You may later be asked to upload data to help debug. ERROR: 3dvolreg.afni Invalid null command. I'm confused on what more I need to install? Is there a way I can get an updated link to the tar file with the relevant software packages needed to run FSFAST? Best, Gillian Grennan

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average lobar cortical thickness
by James Brown 09 Nov '22

09 Nov '22

External Email - Use Caution Dear Freesurfer experts, I would like to know if this procedure is correct. I have cortical thickness data from aparc+aseg for every ROI in DTK atlas (i.e. output of recon-all). I need average cortical thickness in frontal, parietal, temporal, cingulate and occipital lobes. Is it correct to average thickness measurement of every sub lobe roi (e.g. average thickness in frontal lobe = average of: - Superior Frontal - Rostral and Caudal Middle Frontal - Pars Opercularis, Pars Triangularis, and Pars Orbitalis - Lateral and Medial Orbitofrontal - Precentral - Paracentral - Frontal Pole and so on for other lobes... Do we need to correct for the number of vertices in every region when we measure the lobar average thickness? Alternatively, do I need to run these commands to generate lobes then measure thickness in every lobe? # mri_annotation2label --subject subject --hemi lh --lobesStrict lobes # mri_annotation2label --subject subject --hemi rh --lobesStrict lobes # mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \ # --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \ # --annot lobes --base-offset 200 [--base-offset must be last arg] Thank you James

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cortical thickness in frontal lobe
by James Brown 09 Nov '22

09 Nov '22

External Email - Use Caution Dear Freesurfer experts, We are new to Freesurfer. We appreciate your help & apologize if the question is simple. We need cortical thickness in lobes instead of parcellates. Is it correct to take the average of the parcelates from the aparc+aseg.stats file under subjid/stats folder. For example, cortical thickness of frontal lobe = sum of frontal parcellates divided by number of parcallates . Do we need to do any correction such as weighing the surface area measurements ? Thank you James

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Question about a skullstripping error
by dimitra kokkinou 09 Nov '22

09 Nov '22

External Email - Use Caution Dear freesurfer experts, I am analysing some MP2RAGE images on freesurfer and found an error I am unable to correct. After the recon-all finished successfully, I looked at the T1 and brainmask images on freeview and I noticed a skullstripping error on the brainmask volume. On one side of the brain there was also skull (and other non brain parts), and on the other half there was a lot of missing cortex. I tried to change the watershed threshold but this didn't work, I also tried to put control points but most of them were ignored since they were outside of the estimated pial surface. What would be the best way to correct this problem? Regards, DK

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acompcor in fsfast
by Addison, Reuben 09 Nov '22

09 Nov '22

Hi, I am running resting State functional connectivity and I want to run everything in freesurfer and fsfast. I wanted to know is it is possible to run acompcor in fsfast. If so, how do I go about it. Thanks. Get Outlook for iOS<https://aka.ms/o0ukef>

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Help: Vertex Properties
by Sarah Lavelle 09 Nov '22

09 Nov '22

External Email - Use Caution Hi, I’m wondering if there’s a way to get the properties of individual vertices such as: 1)Coordinates 2)Surface area 3)angles 4) Side lengths 5) distance matrix from other vertices And can you get these properties for individual surfaces/ transformations (eg. On the spherical map or flatmap) ? On the FreeSurfer application or else through matlab? Any help would be greatly appreciated, Thanks, Sarah

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Question about freesurfer default settings.
by Katrina Simon 09 Nov '22

09 Nov '22

External Email - Use Caution Hi, I have a dataset i have run with the default settings of Freesurfer 6.0. A reviewer for a paper recently raised the question "Were T1 images warped with the grey matter preserved? Were volumetric images for the amygdala and hippocampus smoothed?" I have tried to look through the archives and freesurfer papers but dont see anything that directly addresses these aspects, and some help would be appreciated. Thank you! Katrina -- Katrina Simon

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FreeSurfer Hippocampus Segmentation Question
by Jun Yeon Won 09 Nov '22

09 Nov '22

External Email - Use Caution Dear Freesurfer experts, I have a question about hippocampal segmentation. For the hippocampal mask after completing recon-all, is it purely gray matter or does it also include some aspects of white matter and others? Please advise. Best, JW

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Calculating Distortion in mris_flatten()
by Sarah Lavelle 08 Nov '22

08 Nov '22

External Email - Use Caution Hi freesurfers, Does anyone know how to measure the distortion of your inflated surface -> flatmap transformation (using mris_flatten)? When being run, the function outputs "final distance error ...%" in the terminal. What exactly does this mean? and how is this calculated? I would like to research optimal cuts for flatmaps, depending on the region of interest (ROI), so we can minimize the distortion of the ROI itself on the 2D map. If anyone has any ideas on how this can be done or is interested in working with me on this, please contact me via < lavells1(a)tcd.ie> Kind regards, Sarah

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Convert image in native coordinate space
by Haiyun Chen 08 Nov '22

08 Nov '22

External Email - Use Caution Hello FreeSurfer Experts, Could you help to tell how can we convert the file lh.pial.native to Nifti file or Dicom file? The file lh.pial.native is generated by FreeSurfer as mentioned in your website: https://secure-web.cisco.com/1OqLwwMukRA3gBsB4xIyWu7jYzQnxoAsxTmCFH4BX5vUNN… <https://secure-web.cisco.com/1ADHgS0v8L4KAY_-4Q1wqkSQ0S5tB-9JDHvuOQr01nK4OE…> Thank you in advance for your help! Best regards Haiyun

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