Freesurfer October 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
95 discussions

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
by fsbuild 16 Oct '23

16 Oct '23

External Email - Use Caution Freesurfer 7.4.1 on Ubuntu 20 uses its own versions of Qt libraries and not the system versions.   So if your setup is looking for or finding system versions of those libraries, then freesurfer may be installed incorrectly and/or could be finding the wrong Qt libraries via use of environment variables like LD_LIBRRY_PATH or Qt*.  (I would try not to set LD_LIBRARY_PATH and Qt environment variables in your shell environment before source’ing the freesurfer setup script). I suggest you remove whatever freesurfer distribution you have on the machine and do a clean re-install of 7.4.1 using the .deb package installer which you can download via the link, https://secure-web.cisco.com/1__PHy5riz1krqgipNavAJIc6annOjWAPD9… If freesurfer was previously installed with the linux package tools then it should work to uninstall it with,$ sudo apt remove freesurfer… answer y to all prompts ... If you unarchived the *.tag.gz file somewhere then “rm -rf” should work on the root freesurfer directory. With the previous freesurfer installation removed, cd to where you downloaded the freesurfer_ubuntu20-7.4.1_amd64.deb and try, $ sudo apt-get -y install ./freesurfer_ubuntu20-7-dev_amd64.deb… wait for install to finish … $ cd$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 ————Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /usr/local/freesurfer/7.4.1FSFAST_HOME       /usr/local/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjectsMNI_DIR           /usr/local/freesurfer/7.4.1/mni $ which freeview /usr/local/freesurfer/7.4.1/bin/freeview$ freeview… freeview should open an empty window … … quit freeview and try opening this example volume … $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz  If you see the attached image, then freeview/Qt is essentially working. - R. On Oct 14, 2023, at 14:14, Andrei Bieger <andreibieger(a)gmail.com> wrote:        External Email - Use Caution        Hi, all!I had to reinstall my VM where I had freesurfer running. Everything was running fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows laptop, where I'm running the version 7.4.1 of Freesurfer.When I downloaded freesurfer it wouldn't run freeview, with the following output: "Application failed to start because no Qt platform plugin could be initialized. Available plugins are: (...)"After some research, I tried "sudo apt install qt5-default" and freeview started running. But the thing is, every time I try loading a subject, the surfaces get completely misaligned with the volumes and the following messages show on the terminal: "Warning: MatrixInverse failed" and "Did not find any volume info". Please, see attached image.<Screenshot from 2023-10-14 15-06-44.png>I tried using Ubuntu 22 and previous versions of freesurfer but the problem persisted. I also found a message with a similar issue on this list, but the user stopped answering so a solution wasn't proposed. There is also a release note from v5.3.0 saying that on Fedora this message would come up, but this is not the case.Any help with that?-- Andrei Bieger_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_glmfit-sim - Clusterwise correction for multiple comparisons.
by Guthrie, Andrew J. 15 Oct '23

15 Oct '23

External Email - Use Caution Hi all, I took the freesurfer course in the recent past, and I am now beginning to run some glm thickness analyses! Currently I am doing a thickness analysis looking at the difference between two groups while controlling for age, and two continuous measures of depression and anxiety. The general commands I run are as follows: mris_preproc --fsgd [fsgd filename] --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --o lh.[filename].thickness.10.mgh mris_preproc --fsgd [fsgd filename] --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi rh --o rh.[filename].thickness.10.mgh mri_glmfit --y lh.[filename].thickness.10.mgh --fsgd [fsgd filename] doss --C contrast.mtx --surf fsaverage lh --glmdir lh_[filename]_fwhm10.glmdir mri_glmfit --y rh.[filename].thickness.10.mgh --fsgd [fsgd filename] doss --C contrast.mtx --surf fsaverage rh --glmdir rh_[filename]_fwhm10.glmdir mri_glmfit-sim --glmdir lh_[filename]_fwhm10.glmdir --cwpvalthresh .05 --cache 2.0 abs --2spaces mri_glmfit-sim --glmdir rh_[filename]_fwhm10.glmdir --cwpvalthresh .05 --cache 2.0 abs --2spaces I noticed that in some analyses there would be no significant clusters when the threshold is set at 2.0 (p<0.01) but if you were to run the same analyses with a threshold at 2.3 (p<0.005) there would be a significant cluster, in the lingual for example. If I go one step further and set the threshold to 3.0 there is also a significant cluster - however the cluster is now in the isthmuscingulate. Am I doing something incorrectly or is this possible? And if so, could you help me understand what is going on here. Best, Andrew

3 2

Use of *inflated resulst from recon-all
by Lesage, Anne-Cecile 15 Oct '23

15 Oct '23

External Email - Use Caution Dear Freesurfer teams I am working on sEEG data to help localize the epileptogenic zone at UTMB. We were wondering with Dr Karas if we could use the *.inflated surface to view better the electrodes in contact with the cortex. Do the *inflated surfaces have the same number of vertices and faces than the *pial ones? Does the *inflated surface respect the same geodesic distance between vertices than the *pial ones? Thank you Best Regards Anne-Cecile Lesage, PhD Research Scientist Department of neurosurgery University of Texas Medical Branch anlesage(a)utmb.edu

2 1

convert to fsaverage
by Sam W 15 Oct '23

15 Oct '23

External Email - Use Caution Hello! I have a volumetric mask of the cuneus and I would like to convert it to a label and then convert that label to fsaverage space. So far I did mri_vol2label --i cuneus.nii.gz --l cuneus.label But how can I now convert cuneus.label to fsaverage? Thanks! Best regards, Sam

3 2

surface based analysis and mask.mgh
by John Anderson 15 Oct '23

15 Oct '23

External Email - Use Caution Dear Freesurfer experts, I am trying to run perfusion data analysis on the brain surface. I registered images to "fsaverage" and concatenated them (following the "petsurfer" pipeline). When I use "freeview" to visualize the concatenated images, they appear correct. However, when I run the "glmfit" command (as shown below), the output appears chopped. Upon checking "mask.mgh", I believe this is the reason the final statistical map is incorrect. I couldn't figure out why this is happening and how to troubleshoot. I would appreciate your guidance mri_glmfit --y lh.cbf.fsaverage.proj0.5sm00.nii.gz --fsgd g1c0.fsgd --C slope-.mtx --surf fsaverage lh --cortex --glmdir lh.cbf Thanks John

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mri_gtmpvc: ROI analisis no psf no rescale, negative or hight uptake.
by Matteo Parodi 15 Oct '23

15 Oct '23

External Email - Use Caution Hello, I'm trying to perform a pet ROI analysis on an image recon from a T1. I have to perform the analysis without normalization and partial volume correction. I'm having problems with regions with few or no voxels which makes me think I'm doing the analysis completely wrong . With this command I obtain negative values for these regions: mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1 .01 --mgx .01 --o $GTM_DIR/gtmpvc_PET.output While with this I get many counts even for regions without voxels: mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1.01 --no-tfe --o $GTM_DIR/gtmpvc_PET.output Could you help me understand my mistake. Thank you very much. Parodi Matteo. I will insert the commands I used before the ROI analysis: recon-all -s Subj -i $IMAGED -all -threads 10 gtmseg --keep-cc --s Subj --xcerseg --o gtmseg100.mgz mri_coreg --s Subj --mov ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --threads 10

2 3

MRIseg2TTypeMap() tissue type for seg 29 Left-undetermined not set
by Óscar Peña-Nogales 15 Oct '23

15 Oct '23

External Email - Use Caution Hi, I'm trying to perform mri_compute_volume_fractions --o output/ --regheader FREESURFER FREESURFER/mri/rawavg.mgz and it apparently works in most of the subjects except in one which gives the following output: $Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname Linux hostname oscar machine x86_64 user oscar setenv SUBJECTS_DIR /home/oscar/Downloads/FS_12/ cd /home/oscar/Downloads/FS_12 mri_compute_volume_fractions --o output/ --regheader FREESURFER FREESURFER/mri/rawavg.mgz --debug outstem output/ regfile (null) regtype 0 segfile aseg.mgz wsurf white psurf pial TempVolFile (null) USF 2 Reading in aseg and surfs from /home/oscar/Downloads/FS_12_69463//FREESURFER Loading /home/oscar/Downloads/FS_12/FREESURFER/mri/aseg.mgz Filling empty voxels with extracerebral CSF (if not there already), nDil=3 Computing registration from header -0.98185 0.17682 -0.06858 199.82191; -0.11189 -0.24810 0.96225 50.90987; -0.15313 -0.95246 -0.26338 303.22836; 0.00000 0.00000 0.00000 1.00000; t = 15.599 Computing PVF (USF=2, resmm=0.500000) MRIhiresSeg(): filling unknowns with 257 ERROR: MRIseg2TTypeMap() tissue type for seg 29 Left-undetermined not set Are you familiar on how to solve this error? In previous Q&A I saw this happened in PETsurfer to some people, but that solution does not seem to work in this case (or might might not be doing it correctly) Any help is very welcome. Thank you in advance Óscar

2 1

Problem with tkregister2/tkregisterfv
by Nadvar, Negin 15 Oct '23

15 Oct '23

External Email - Use Caution Good afternoon, I’m trying to run “tkregister2” in the following code for a manual registration correction: tkregister2 --mov ./fMRI_run1.nii.gz --reg ./Reg.lta --surfs --sd ${SubjectsFolder} The above command works fine in older versions of FreeSurfer, but with the new version that I have, I’m getting the following error: Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. I get the same error with "tkregisterfv". Here’s more info about my system, in case it helps. OS: Linux Ubuntu 18, FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460, Python version: Python 3.11.4, FSL version: 6.0.7.1 Please let me know if there's a known solution for this issue. Thank you, Negin

2 1

Re: [Freesurfer] MANCOVA + Posthoc Testing Design Matrix Setup
by Cristina A. F. Román 15 Oct '23

15 Oct '23

External Email - Use Caution Hello, I am looking to run a MANCOVA to examine cortical gray matter differences across three groups (accounting for several covariates), and I was hoping to get input on whether I am setting up my design matrix correctly. Groups: 3 Covariates: Age (demeaned), disease duration (DD; demeaned), sex Simplified Example: Group EV1(Grp1) EV2(Grp2) EV3(Grp3) EV4(age) EV5(DD) EV6(sex) 1 1 0 0 0.25 0.75 -1 1 1 0 0 0.25 0.25 -1 1 0 1 0 -0.75 -0.25 1 1 0 1 0 0.5 -0.75 1 1 0 0 1 -0.5 0.5 1 1 0 0 1 0.25 0.25 -1 Questions: 1. Is this an appropriate way to do a three-group comparison with covariates? Or, is it better to just run three separate t-tests (including covariates)? 2. Regarding post-hoc testing, would I just do three separate t-tests? This issue here, I imagine, is that the individual t-test results may not reflect the original MANCOVA results (e.g., post-hoc testing reveals a new significant area that was not significant in the MANCOVA). 3. One other option is to run the initial MANCOVA within a statistical program (i.e., using global cortical gray matter volumes) and then follow up with postdoc testing within FSL (i.e., t-tests). Would this make sense? Thanks in advance for your time and help, Cristina

2 1

Question about mri_nu_correct.mni
by ruifeng14＠gmail.com 15 Oct '23

15 Oct '23

External Email - Use Caution Hi all, I am running Freesurfer 7.3.2 on T1 images (LPI orientation) with 176*256*256 FOV, 1mm isotropic resolution. I saw that the Ants N4 bias correction is done after the FOV is expanded to 256*256*256, not on the original image. Shouldn't the zeros in the expanded image affect the bias correction? Thanks. Best, Ruifeng

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Freesurfer October 2023