Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Curvature differences between 7T and 3T images
by Samuel Paré 24 Mar '22

24 Mar '22

External Email - Use Caution Hello, We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference? Thanks, Samuel [image: image.png] -- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal

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Updated Ubuntu 18 VM image with Freesurfer 7.2.0 release pre-installed
by fsbuild 23 Mar '22

23 Mar '22

External Email - Use Caution The Ubuntu 18 VM image with the terminal shell environment set out of the box to use the pre-installed freesurfer 7.2.0 release - is back online.  While the functionality of the release is unchanged, the new image is:- named with 7_2_0 to distinguish it from future releases- a bit smaller in size and may run faster depending upon your hardware- expanded a bit differently Please see the wiki page for details, https://secure-web.cisco.com/1yIC-PbRjEF1VSkLF8fML6h4gueEGDMqWNEbYP-pGBkGm0… Happy to address any inquiries. - R.

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mri_convert: possible bug converting float to int
by Gesierich, Benno Gerhard Dr. 22 Mar '22

22 Mar '22

External Email - Use Caution Hello FreeSurfer Developers, I converted a label map (<in volume>), given as Nifti image of type float32 and located in Freesurfer conform space, back to native space using the native T1 in Nifti format and with type int16 as reference <reference volume> . During conversion, the datatype was automatically converted to that of the reference T1. Unfortunately, the labels changed during this conversion, probably because of applying a scaling (slope), which is not saved correctly to the Nifti header. I come to this conclusion, because the maximum label in the output has the maximum value, possible with int16 datatype, i.e. 32767 Here the exact command I used: mri_convert -rt nearest -rl <reference volume> <in volume> <out volume> The problem of changed labels in the output can be avoided by using the —no change option, which keeps the datatype of the input: mri_convert --nochange -rt nearest -rl <reference volume> <in volume> <out volume> I used Fresurfer 7.2.0 Best Regards, Benno Gesierich

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TRACULA longitudinal - weird tracts
by Donovan Roediger 21 Mar '22

21 Mar '22

External Email - Use Caution Hello Anastasia, I ran TRACULA (7.2.0) twice on the same dataset, once as cross-sectional and once as longitudinal. The cross sectional tracts look OK, but the longitudinal output looks very bad for every subject. Below are summaries of my workflows along with links to screenshots of the resulting tracts. Can you tell what I'm doing to mess up the longitudinal stream? Cross sectional TRACULA: 1) Structural and diffusion data preprocessed using HCP 4.0.1 (which includes cross-sectional recon-all with FS 6.0) 2) Thalamic segmentation was run using FreeSurfer 7.2.0. 3) Cross sectional TRACULA (7.2.0) was run using the HCP-cleaned diffusion data. Default settings used except doeddy=0 because eddy was run as part of HCP preprocessing. IMAGE: https://secure-web.cisco.com/13BZ6YlVnYcAOxNoC1FBf0K8tfLvVUgG_XzJ51MPZJ5fE6… Longitudinal TRACULA: 1) Structural and diffusion data preprocessed using HCP 4.0.1 (which included cross-sectional recon-all with FS 6.0). 2) Longitudinal recon-all was run under FreeSurfer 6.0 starting with the HCP FreeSurfer cross-sectional outputs. 3) Thalamic segmentation was run on the ".long" subjects using FreeSurfer 7.2.0. 4) Longitudinal TRACULA (7.2.0) was run using the HCP-cleaned diffusion data. Default settings used except doeddy=0 because eddy was run as part of HCP preprocessing. IMAGE: https://secure-web.cisco.com/1us4Dr6uNFzuOYt72IbrjF1_SvArR22k16JUpH4ZBPgF2W… Thanks so much! Donovan -- Donovan Roediger Neuroimaging Analyst | Psychiatry | psychiatry.umn.edu University of Minnesota Medical School | med.umn.edu | 612-626-5064 staff bio <https://secure-web.cisco.com/1IdZ5gFMBKeiXOXZZl8u_Lmu2Itqgjp8vqJbAswnHrkh98…> | he, him, his

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Gcut error: gcutted brain is much smaller than the mask
by Begüm Cerrahoğlu 21 Mar '22

21 Mar '22

External Email - Use Caution Dear developers, I am trying to clean up the extra dura left after skullstripping. Watershed parameter does not prove to be much helpful and when I try gcut I get the error below. I checked the release notes of freesurfer 5.1 and mri_gcut is not run by default. In the archives I came across this exact problem before, under this message: msg18797 <https://secure-web.cisco.com/1Gix4yHAghaLSVAVD-cOy4QmehGJB3UyVkUd5GwVNmFNq_…> However, there was not an end solution available in the archived email exchange. I am not interested in cerebellum and am okay with cutting the cerebellum out of the brain mask as long as it does not interfere with being able to distinctly separate cortex from cerebellum in the following steps. From skullstripping tutorials,I have read that one should not start erasing cerebellum from the brainmask directly and was wondering if you could let me know why? In sum, are there important reasons to keep the cerebellum despite only being interested in analyzing the cortex? If not, could you please let me know what could be the reason for gcut's failure and if there is anyway to disable failure detection so I can see if the gcutted brain is usable? >> " rm -f brainmask.gcuts.mgz >> mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz >> brainmask.gcuts.mgz >> >> INFO: Care must be taken to thoroughly inspect your data >> when using mri_gcut. In particular, inspect the edges of >> gm and cerebellum for over-aggressive cutting. >> Add -segmentation brainmask.gcuts.mgz to the tkmedit >> command string to view the voxels which gcut has removed. >> >> reading mask... >> white mean: 107.529232 >> threshold set to: 107.529232*0.400000=43.011693 >> calculating weights... >> doing mincut... >> now doing maxflow, be patient... >> g-cut done! >> post-processing... >> post-processing done! >> masking... >> ** Gcutted brain is much smaller than the mask! >> ** Using the mask as the output instead! >> >> cp brainmask.auto.mgz brainmask.mgz " 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. 2) Platform: Linux Mint 20.2 Thank you greatly for your time and efforts. Kindest regards, Begum Cerrahoglu

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Trouble with fs_install_mcr script
by Andrei Bieger 19 Mar '22

19 Mar '22

External Email - Use Caution Hello, everyone, I`m having trouble installing the MatLab Runtime 2014b as required for running the new hippocampal subfields pipeline. The "fs_install_mcr 2014b" command returns me the message below: *andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ fs_install_mcr 2014b % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed100 10 100 10 0 0 2 0 0:00:05 0:00:04 0:00:01 2Archive: installer.zip End-of-central-directory signature not found. Either this file is not a zipfile, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive.unzip: cannot find zipfile directory in one of installer.zip or installer.zip.zip, and cannot find installer.zip.ZIP, period.* Then I tried running the specific line of the script to download the file so I could take a look at it: *andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ curl --location https://secure-web.cisco.com/1EdMsU-hQ3VZ1K97z-aS22OCA3G_bwtGWsa4wkPQY7WCPE… <https://secure-web.cisco.com/1EdMsU-hQ3VZ1K97z-aS22OCA3G_bwtGWsa4wkPQY7WCPE…> -o installer.zip % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed100 10 100 10 0 0 161 0 --:--:-- --:--:-- --:--:-- 161andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ file installer.zipinstaller.zip: ASCII text* *andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ unzip installer.zipArchive: installer.zip End-of-central-directory signature not found. Either this file is not a zipfile, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive.unzip: cannot find zipfile directory in one of installer.zip or installer.zip.zip, and cannot find installer.zip.ZIP, period.* It does not recognize it as a .zip file, and the Ubuntu Archive Manager won`t recognize it either: *"An error occurred while loading the archive."* I know this is more of a Linux/Matlab issue than a freesurfer one. But I wonder if anyone else is facing this issue? Might that be a problem with the curl package, Matlab support to older Runtime versions or my Linux distro? Also, could you please give me instructions on where to install the file manually from https://secure-web.cisco.com/1f47DuzXT9iWt3QZ-FmPoYU6PuX8nCvVAsdXGDH3F_QY6C… ? Thank you! -- Andrei Bieger

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Tracula 6.0 or 7.2 - sub in alternative metric maps
by Thorn, Kathryn 18 Mar '22

18 Mar '22

External Email - Use Caution Hi Freesurfer/Tracula experts, I would like to use my own diffusivity and anisotropy maps (FA, MD, etc) with Tracula as opposed to the maps generated by dtifit during the course of trac-all -prep. I see that there is a -notensor option to stop dtifit from producing metric maps; however I am wondering if there's any way to get Tracula to recognize alternative metric maps that I supply to it. My main goal is to sub in my own metric maps for the purposes of having Tracula generate tract profiles (pathstats.byvoxel.txt) with metric maps I generated via an alternative fitting method to dtifit. Is there any way to do this? Additionally, is there any way to have Tracula perform these same types of analyses with kurtosis maps or other types of dMRI data? I've been working mainly with Tracula 6.0 as I have received an as yet unresolved mri_binarize error with Tracula 7.2. However, I am curious if the above is possible with either or both versions. Thank you! Kayti Thorn (she/her) Database Specialist Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425

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Re: [Freesurfer] Hippocampal segmentation Matlab crash
by Caitlin R Bowman 18 Mar '22

18 Mar '22

External Email - Use Caution Tried it, but I still get the same error. -- Caitlin Bowman, Ph.D. Assistant Professor of Psychology University of Wisconsin-Milwaukee From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, March 8, 2022 at 3:18 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash Hi Cait, Before running the command, can you try unsetting the LD_LIBRARY_PATH variable? You can do this in bash with: unset LD_LIBRARY_PATH or in cshell with: unsetenv LD_LIBRARY_PATH best, Andrew From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Caitlin R Bowman <bowman2(a)uwm.edu> Date: Tuesday, March 8, 2022 at 3:14 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal segmentation Matlab crash External Email - Use Caution Hello, I am trying to run the hippocampal segmentation used in freesurfer 7. I have tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am running on a computing cluster, not locally. The same code works fine on my local computer. The managers of the computing cluster have tried to help but are stuck themselves. Find the command that I run below followed by the full error log. Best, Cait Command: segmentHA_T2.sh sub-110033 $ANATDIR/sub-110033_T2w.nii.gz T2 0 Error log: ------------------------------ USER bowman2 HOST compute-081.mortimer PROCESSID 11325 PROCESSOR x86_64 OS Linux Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux ------------------------------ #-------------------------------------------- #@# Hippocampal Subfields processing (T2) left Thu Feb 24 14:14:35 CST 2022 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/os/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sharedapps/LS/psych_imaging/fsl/6.0.4/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/sys/os/glnxa64::/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/vtk/lib/vtk-5.6/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/tcltktixblt/lib/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/KWWidgets/lib/KWWidgets:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/mni/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib ------------------------------------------------------------------------ std::terminate() detected at Thu Feb 24 14:14:37 2022 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Default Encoding : UTF-8 GNU C Library : 2.17 stable MATLAB Architecture: glnxa64 MATLAB Root : /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Linux 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 Processor ID : x86 Family 6 Model 63 Stepping 2, GenuineIntel Fault Count: 1 Abnormal termination: std::terminate() Register State (captured): RAX = 0000000000000000 RBX = 00002baa657204e8 RCX = 0000000000000000 RDX = 00002baa6570f758 RSP = 00002baa93ffb0b0 RBP = 00002baa93ffb470 RSI = 00002baa654c3fb3 RDI = 00002baa93ffb0c0 R8 = 0000000000000000 R9 = 00002baa60271f90 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 00002baa65730520 R13 = 00002baa93ffc0b0 R14 = 00002baa93ffc090 R15 = 00002baa93ffc470 RIP = 00002baa65422f4e EFL = 0000000000000000 CS = 0000 FS = 0000 GS = 0000 Stack Trace (captured): [ 0] 0x00002baa65422f4e /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00966478 _ZN2fl4diag5linux12context_base12capture_dataEv+00000030 [ 1] 0x00002baa65420424 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00955428 [ 2] 0x00002baa740ef0f5 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00868597 [ 3] 0x00002baa740f12ca /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877258 [ 4] 0x00002baa740f13c1 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877505 [ 5] 0x00002baa740f1743 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878403 [ 6] 0x00002baa740f17b3 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878515 [ 7] 0x00002baa5ffe4a06 /lib64/libstdc++.so.6+00387590 [ 8] 0x00002baa5ffe4a33 /lib64/libstdc++.so.6+00387635 [ 9] 0x00002baa5ffe4c53 /lib64/libstdc++.so.6+00388179 [ 10] 0x00002baa60fe3822 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so+00325666 _ZN2fl4i18n14MessageCatalog17GetMessageCatalogERKNS0_9CatalogIDERKNS0_8MwLocaleE+00001186 [ 11] 0x00002baa60fe4113 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so+00327955 _ZN2fl4i18n14MessageCatalog11get_messageERKN13resource_core9BaseMsgIDERKNS0_8MwLocaleE+00000051 [ 12] 0x00002baa6589bf57 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01482583 [ 13] 0x00002baa6589ae6f /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01478255 [ 14] 0x00002baa65832a44 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01051204 _Z14mxWarningMsgIdRKN13resource_core9BaseMsgIDE+00000052 [ 15] 0x00002baa74443a95 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwjmi.so+01100437 [ 16] 0x00002baa74443d2f /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwjmi.so+01101103 _Z50mljInitFirstCrackSignalHandlerIfJavaAlreadyStartedv+00000015 [ 17] 0x00002baa740c5855 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00698453 [ 18] 0x00002baa740b64ec /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00636140 [ 19] 0x00002baa740a2cdd /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00556253 [ 20] 0x00002baa607adea5 /lib64/libpthread.so.0+00032421 [ 21] 0x00002baa60ac0b0d /lib64/libc.so.6+01043213 clone+00000109 If this problem is reproducible, please submit a Service Request via: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/118J8xb20RT93i80kANwrgAlajqHThJt-SNhm0DJUsUTVUk…<https://secure-web.cisco.com/1sWwW4ZPn37eyMEn2XV0J_7cDBgIf6OqYIkEUaQB3x0FDi…> A technical support engineer might contact you with further information. Thank you for your help.** This crash report has been saved to disk as /home/bowman2/matlab_crash_dump.11396-1 ** MATLAB is exiting because of fatal error /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/run_segmentSubjectT2_autoEstimateAlveusML.sh: line 40: 11396 Killed /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/segmentSubjectT2_autoEstimateAlveusML sub-CC110037 /home/bowman2/Data/camcan/fs_camcan/ /raid-18/LS/bowman2/camcan/imaging/anat/sub-CC110037/sub-CC110037_T2w.nii.gz 0.333333333333333333333333333333333333 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/AtlasMesh.gz /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/AtlasDump.mgz /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 T2 '/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/fs_run_from_mcr /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/' 0 1 0 @#@FSTIME 2022:02:24:14:14:35 run_segmentSubjectT2_autoEstimateAlveusML.sh N 18 e 1.65 S 0.13 U 1.19 P 80% M 67608 F 0 R 19447 W 0 c 32 w 559 I 0 O 84720 L 5.00 5.06 4.81 @#@FSLOADPOST 2022:02:24:14:14:37 run_segmentSubjectT2_autoEstimateAlveusML.sh N 18 5.00 5.06 4.81 Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at Thu Feb 24 14:14:37 CST 2022 -- Caitlin Bowman, Ph.D. Assistant Professor of Psychology University of Wisconsin-Milwaukee

2 1

run_samseg output folder permissions error
by daedalus39＠aol.com 18 Mar '22

18 Mar '22

External Email - Use Caution Dear experts, Having installed Freesurfer on WSL2, I was able to get the basic FS segmentation to run without error. However, when I tried to run_samseg on a single T1 image, I received the following error message (permissions denied creating the "output folder") Is there anything in the trace (below) that provides a clue? daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ run_samseg --input o_ADNI_002_S_4654__MRI-m072.nii --output /T1-only -samsegOutput/ Traceback (most recent call last): File "/usr/local/freesurfer/7-dev/python/scripts/run_samseg", line 67, in <module> os.makedirs(args.outputDirectory, exist_ok=True) File "/usr/local/freesurfer/7-dev/python/lib/python3.6/os.py", line 220, in makedirs mkdir(name, mode) PermissionError: [Errno 13] Permission denied: '/T1-only-samsegOutput/'

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Extraction of CC Labels and Conversion to FSL MNI Space
by Hua, Jessica 17 Mar '22

17 Mar '22

External Email - Use Caution Hi FreeSurfer, I am trying to extract CC subregion labels from aparc+aseg.mgz (ids: 251-255) into a format that is compatible with MNI space in FSL. I was planning on extracting CC labels and then converting the labels from fsaverage space to MNI space. I first tried to extract the 5 separate CC labels using the command: mri_vol2label --c aparc+aseg.mgz --id 255 --l 255.label. When viewed in FreeView, the labels were spotty looking. Did I do this mgz to label extraction correctly? [cid:7dee544f-74a8-43d0-be89-9af1a0c74e2f] And also do you have a recommended code to convert FreeSurfer CC subregions into MNI space ROIs for FSL? Best, Jessica

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