Freesurfer September 2023

freesurfer@nmr.mgh.harvard.edu

71 participants
88 discussions

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

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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

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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

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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

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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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Fwd: Postdoctoral fellowship in radiopharmaceutics: Innis at NIH
by Douglas N. Greve 28 Sep '23

28 Sep '23

External Email - Use Caution Please contact Bob with inquiries. -------- Forwarded Message -------- Subject: Postdoctoral fellowship in radiopharmaceutics: Innis at NIH Date: Thu, 28 Sep 2023 15:11:57 +0000 From: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> To: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> External Email - Use Caution This fellowship is for someone with experience in radiochemistry who seeks training in molecular imaging. The rationale underlying this combined program is that all leading PET radiochemists are also very knowledgeable about PET imaging, including pharmacology, animal imaging, and regulatory requirements for human studies. The goal of this combined program is to train future leaders in the field of PET molecular imaging. Please forward the attached advertisement to relevant and interested parties. Bob Innis ************************************ Robert B. Innis, MD, PhD Chief, Molecular Imaging Branch National Institute of Mental Health 10 Center Drive, MSC-1026 Bldg. 10, Rm. B1D43 Bethesda, MD 20892-1026 Tel: 301-594-1368 Fax: 301-480-3610 Email: robert.innis(a)nih.gov <mailto:robert.innis@nih.gov> Branch Administrative Manager: Elizabeth Alzona Tel: 301-594-1089 Email: alzonae(a)irp.nimh.nih.gov <mailto:alzonae@irp.nimh.nih.gov> http://secure-web.cisco.com/1cu2NiF_yAv_LRbeG3tSLrzRwgvhifMD6iasg9KS9KOx7k7… <http://secure-web.cisco.com/1H3yqgPC4k8FXcyKY0ko-27zDzniCxLR2ug6swsJ7KoOpcr…> ************************************

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Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg
by fsbuild 28 Sep '23

28 Sep '23

External Email - Use Caution   Thanks for reporting this.  This posting indicates there is a difference in defining that for arm64 compared to intel architectures,  https://secure-web.cisco.com/1FTmSa1QjGMsQB8Xf5Zs… We will look into it along with producing an updated arm64 build.  You could try making the change described in the posting in the SynthSeg code if you like. You will not encounter that error in any existing/previous release, 7.4.1 ... 7.3.2 as you are using a new arm64 development build which is post the 7.4.1 release. - R. On 9/28/23 07:20, Conrad, Julian (Julian.Conrad(a)medma.uni-heidelberg.de) wrote: Hello again FreeSurfer Developers,   I'm attempting to do a surface reconstruction from a GRE magnitude image using recon-all-clinical.sh As was stated before, there seem to be issues with the current Mac processors. so I downloaded the dev version (https://secure-web.cisco.com/1k8eRfZmZxutbzTfMi5opOvIJvAU3A9yjOgbNxek0vGGGW…) as was suggested by your team. Now it started to run. But I got this error:   File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/numpy/__init__.py", line 320, in __getattr__     raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'float128' Error in SynthSeg   (see also attached recon log)   My numpy version is 1.26, python 3.9.6   I tried to change the float specifications using this but this did not do the job https://secure-web.cisco.com/1Nw2CoSnBRIpwTK-GWDBJpxLeD53b5CAywKvOfsawRYQsC…   Do you have an idea how to fix this?   Will this also occur if I opted for freesurfer 7.3.2? I am a little hesitant do install the older version just yet..   Best regards, Julian     Mit freundlichen Grüßen   Dr. med. Julian Conrad       Oberarzt | senior physician Sektion Neurodegeneration | Division of Neurodegeneration Neurologische Klinik | Department of Neurology Universitätsmedizin Mannheim | University Medicine Mannheim Medizinische Fakultät Mannheim | Medical Faculty Mannheim Universität Heidelberg| Heidelberg University Theodor-Kutzer-Ufer 1 - 3 D-68167 Mannheim Tel.  +49 621 383-9025 E-Mail: julian.conrad@umm.de https://secure-web.cisco.com/1Ys12d1Q7EjaOXQJ3u43f5YMcfnSzuXxz579PUioZIBnkd…   Universitätsklinikum Mannheim GmbH Geschäftsführer: Freddy Bergmann, Prof. Dr. med. Hans-Jürgen Hennes | Aufsichtsratsvorsitzender: Dr. Peter Kurz Handelsregister-Nr. 7331 Mannheim | Sitz und Gerichtsstand: Mannheim   Medizinische Fakultät Mannheim der Universität Heidelberg Dekan: Prof. Dr. med. Sergij Goerdt ---------- Diese E-Mail enthält möglicherweise vertrauliche und/oder rechtlich geschützte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den Absender und löschen Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail ist nicht gestattet. Universitätsmedizin Mannheim universitär - modern – menschlich     Von: fsbuild <fsbuild(a)contbay.com> Datum: Mittwoch, 27. September 2023 um 00:55 An: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Cc: "Conrad, Julian" <Julian.Conrad(a)medma.uni-heidelberg.de> Betreff: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg     Besides patching the python distribution, another option available now is the development arm64 build for silicon Macs with an M1, M2 processor.  But this is not a release build and so has not been tested like a stable release.  The dev builds are currently ~3 months post the 7.4.1 release from back in June of this. year.  We’d be happy to hear how it goes if you try it.  The download links are below.   - R. https://secure-web.cisco.com/1k8eRfZmZxutbzTfMi5opOvIJvAU3A9yjOgbNxek0vGGGW… https://secure-web.cisco.com/1ISJip9DWoHbMeApDNRqD9f2lcyluijXFKQrQuGiqB8rzp…     On Sep 26, 2023, at 18:01, Sorby-Adams, Annabel <ASORBY-ADAMS(a)mgh.harvard.edu> wrote:           External Email - Use Caution           Hi Julian,   I have managed to run recon-all on my Apple M1 macOS Ventura using the 7.3.2 version of Freesurfer. It does not work on 7.4.2 or dev versions, however. These instructions were posted in a previous correspondence from fsbuild, but reposting here for anyone else having the same issue:     You may not be able to run these commands without sudo/admin permissions on your machine. 1) Download the tensorflow-2.4.1-py3-none-any..whl from, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://drive.google.com/file/d/15Qeve5FIA137KON67ehKIOyXy1N0PbAC/view?us… 2) Check the download is OK with the md5 command in the terminal window, $ md5 tensorflow-2.4.1-py3-none-any.whl MD5 (tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4 DO NOT PROCEED UNTIL YOU GET THE ABOVE OUTPUT FROM the md5 command. 3) Setup the Freesurfer 7.3.2 environment (shown here as installed via ..pkg file under /Applications) and verify the path to fspython is from the 7.3.2 release, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.3.2-20220803-878457d -------- .... environment variable settings output ... $ which fspython /Applications/freesurfer/7.3.2/bin/fspython 4) Uninstall the existing tensorflow package with, $ sudo $FREESURFER_HOME/python/bin/python3 -m pip uninstall tensorflow .... apart from any warnings you should see the output ... Successfully uninstalled tensorflow-2.4.1 5) Install the package downloaded above.  This command assumes the package is in the current directory where the command is run. $ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip install ./tensorflow-2..4.1-py3-none-any.whl .... apart from warnings and output about requirements (which should all be satisfied) ... .... you should see tensorflow was updated ..... Successfully installed tensorflow-2.4.1 CHECK THE UPDATE: $ which fspython /Applications/freesurfer/7.3.2/bin/fspython $ fspython >>> import sys, os >>> import tensorflow >>> You should see the prompt return to ">>>" after the import of tensorflow with no errors reported.  Hit Ctrl-D to escape the python session.  The update should now be complete.   Once you have done this you should be able to run recon-all via 7.3.2. Hope this works! Annabel   From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Date: Tuesday, 26 September 2023 at 17:35 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg         External Email - Use Caution         Dear Julian, I believe this is a problem with SynthSeg not being compatible with the new microprocessor in MAC computers. Our software engineers are looking into solutions to this. Sorry for the inconvenience, Eugenio   -- Juan Eugenio Iglesias http://secure-web.cisco.com/15K8tGUf8tZtMuq_5Nf3tfTFHYuzBUKgcIyghX2882Gja50…   From: freesurfer-bounces@nmr.mgh..harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Conrad, Julian <Julian.Conrad(a)medma.uni-heidelberg.de> Date: Tuesday, September 26, 2023 at 4:38 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg         External Email - Use Caution         Hello FreeSurfer Developers,   I'm attempting to  do a surface reconstruction from a GRE magnitude image using recon-all-clinical.sh When I am running the pipeline, I get the following error:   Illegal instruction Error in SynthSeg   neuroadmin@medma0236 ~ % recon-all-clinical.sh /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii RC026_sub-010_ses-mri01 8 /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer #-------------------------------------------- #@# recon-all-clinical Di 26 Sep 2023 21:53:31 CEST   mri_convert /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz  reading from /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii... TR=49.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.997386, 0.00125151, 0.0722456) j_ras = (2.37011e-10, 0.99985, -0.0173204) k_ras = (-0.0722564, 0.0172751, 0.997236) writing to /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz...   Illegal instruction  Error in SynthSeg   1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1 2) Platform: MacOS X Darwin   Hope this information is sufficient and there is an easy solution. Best regards, Julian   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1WzT07ap5K7I2AhkWT_MIV_xAyZTUYP9UShEb3DDRK757O…

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[WARNING: ATTACHMENT UNSCANNED]Errors in recon-all for post-operative T1 images
by Jingping Xie (SBS) 27 Sep '23

27 Sep '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare the pre-operative (pre-op) and post-operative (post-op) anatomical images for a group of patients who underwent brain tumor resection. During the operation, part of the brain tissue and the skull were removed, and I would like to mark or label the removed/changed region (both cortical and subcortical) in the pre-op intact reconstructed brain. For one sample subject (tumor on the left side), I have completed the recon-all for the pre-op T1 images without any error reported. However, for the post-op images, the key volumes such as T1/brainmask/wm.mgz were generated from recon-all steps but failed in getting almost all surfaces. The related recon-all log and T1.mgz can be found in the attachment. I wonder whether (and how to) a detailed quality check or troubleshooting could solve such recon-all errors? Could I reconstruct the post-op brain when part of the structure is missing and reach my original goal? I used FreeSurfer 7.4.1 on MacOS Ventra 13.0. Thank you for your kind assistance. Best regards, Jodie ****************************************************************************************************** Jodie J. XIE, Ph.D. School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong [40 Logo_FINAL_Email template]

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Re: [Freesurfer] Running MATLAB on a MAC PRO
by fsbuild 26 Sep '23

26 Sep '23

External Email - Use Caution  You can try using the fs_install_mcr script to install the matlab runtime environment instead of using a generic or full install of Matlab on the machine.  Below the PATH to FREESRUFER_HOME is listed as /Applications/freesurfer/7.4.1, but you should change it to be whatever you installed on your machine.   The 7.4.1 release was tested with R2019b $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh <... output showing SUBJECTS_DIR and other environment variables> $ cd  $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b I think that sets things up so the libmwm* libraries are in the freesurfer tree under the path, $FREESURFER_HOME/MCRv97/bin/glnxa64.- but you should check that path. Then you can try adding the path you verified, e.g., $FREESURFER_HOME/MCRv97/bin/glnxa64,  to the head of LD_LIBRARY_PATH and remove any other entries to a different MATLAB distribution. - R.. On Sep 26, 2023, at 18:13, Alan Francis <alandarkenergy(a)gmail.com> wrote:        External Email - Use Caution        Hi All :I just bought a 2023 MAC PRO with an M2 Ultra Chip for my lab. It's running macOS Ventura. I have installed MATLAB on it but it refuses to run in a terminal or from the Applications folder.MATLAB runs perfectly fine on my other Linux machines.The MATLAB website has very little, if outdated, help.Have any of you encountered this problem?Thanks,Alan-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of NeuroscienceUniversity of Texas, School of MedicineRio Grande ValleyTexas.                                                                                                           _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer September 2023