Freesurfer

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30130 discussions

fsaverage folder
by yunus soleymani 29 Nov '23

29 Nov '23

External Email - Use Caution Hello Freesurfers, I am currently using the parallel recon-all code in Freesurfer to analyze my subjects. While reviewing the results folder, I came across a folder named 'fsaverage' which had a locked icon next to it, along with the folders for each individual subject. I am curious to know what this folder is and how it could be useful. Thank you for taking the time to answer my question. Best regards,Yunus --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------

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Cannot locate reg.lta
by Mirsol Choi 28 Nov '23

28 Nov '23

External Email - Use Caution Hi there, I am currently trying to run vol2subfield command that allows us to get a registration between an input volume (ie. FA map) to a subfield volume (hippocampus segmentation). Upon tying vol2subfield --help, this was the message provided: "vol2subfield (run with --help to get more info) Required inputs --i input volume --sf subfield volume : full path or relative to subject/mri --reg reg.lta : registration that maps input volume to conformed Outputs --o output volume --outreg outreg.lta : registration between invol and subfield --stats stats.dat : run mri_segstats with --sum stats.dat output --avgwf avgwf.dat : run mri_segstats with --avgwf avgwf.dat output --avgwfvol avgwfvol : run mri_segstats with --avgwfvol avgwfvol output Other options --ctab ctab : color table to use with mri_segstats. Default is /home/masterslab/freesurfer/FreeSurferColorLUT.txt --nearest : use nearest neighbor interpolation (default) --trilin : use triliear interpolation --cubic : use cubic interpolation --tmp tmpdir : for debugging These are meant to make it easy to interface with the various subfield segs produced by FS --lh.hippoamyg : set subfield to lh.hippoAmygLabels-T1.v21.mgz --rh.hippoamyg : set subfield to rh.hippoAmygLabels-T1.v21.mgz --lh.hbt : set subfield to lh.hippoAmygLabels-T1.v21.HBT.mgz --rh.hbt : set subfield to rh.hippoAmygLabels-T1.v21.HBT.mgz --thalamus : set subfield to ThalamicNuclei.v10.T1.mgz --brainstem : set subfield to brainstemSsLabels.v12.mgz vol2subfield 7.4.1 vol2subfield provides routines that make it easier to integrate arbitrary volumes with volumes that share a RAS space ("header registration") with the orig volume in the FreeSurfer mri folder. This script was written to manage "subfield" segmentations (eg, hippocampal, amygdalar, thalamic, and brainstem), but it can be used much more generally. The input registration is the LTA registration between the input volume and the orig.mgz (eg, computed with bbregister or mri_coreg). IF THIS REGISTRATION IS INACCURATE THEN THE OUTPUT OF THIS SCRIPT WILL BE WRONG!! To check the input registration run tkregisterfv --mov invol --reg reg.lta --surfs This script can have three types of outputs: 1. To get a registration between an input volume and a subfield volume vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz --outreg outreg.lta outreg.lta will map fa.nii.gz to rh.hippoAmygLabels-T1.v21.HBT.mgz. Note that the "subfield" volume can be anything that shares a RAS space with the orig.mgz (eg, orig/001.mgz). It does not need to be a segmentation volume. 2. To map the input volume into the subfield volume space vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz --o fa.rh.hbt.mgz fa.rh.hbt.mgz will be the fa.nii.gz sampled into the space of rh.hippoAmygLabels-T1.v21.HBT.mgz (ie, it will be in voxel-for-voxel registration). Again, the "subfield" volume can be anything that shares a RAS space with the orig.mgz (eg, orig/001.mgz). It does not need to be a segmentation volume. This volume is appropriate for running mri_segstats. Note that there is not an output registration, but, if you want to save it, just use --outreg as above. 3. To compute segmentation statistics of the input volume vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz \ --o fa.rh.hbt.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol avgwfvol.mgz This will create three files (but you do not need to specify all of them) using mri_segstats (and excluding the 0 segmentation). See mri_segstats --help for what each of these outputs mean. Note that there is not an output registration, but, if you want to save it, just use --outreg as above. For information about the subfields created by FS, see https://secure-web.cisco.com/17XF0ZnFdoeIqVKRGWwoBOtca4h4jeD6xXfzmAx0GK1TEH… http://secure-web.cisco.com/1r9hdzClzfpb9wkcYJZzj-5x_1dXL8bvIXvPjcusisxNujt… https://secure-web.cisco.com/1zX2UZrV6ZpJQDeBcxFrsoi9bFd1JnN4YH4d0ttvaTwhHg…" In all 3 examples of codes provided here, they all require an input of "reg.lta." However upon searching all of my freesurfer folder or recon outputs, we do not see any file names "reg.lta." Is there a process I must take to create this file? If someone could answer this question for me, I will be eternally grateful. Best, M

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issue with mri_vol2surf
by Atena Akbari 28 Nov '23

28 Nov '23

External Email - Use Caution Dear freesurfer team, I want to overlay the activation map that I got from SPM on the inflated surface. The command I use is: "mri_vol2surf --mov spmT_funcmap.nii --ref subj01/mri/orig.mgz. --reg tk.dat --hemi rh --o flodername" in which, I got the registration file (tk.dat) by aligning my functional mean image to the orig.mgz in tkregisterfv. now the problem is when I overlay the activation map on the inflated surface, I can only see the voxels with positive t-values. I can't see the negative ones. I cannot change the threshold values provided by "configure overlay" to negative values. Also, changing the "z-score" option next to the overlay configuration doesn't make any difference. can you help me with this, please? Thanks a lot, Atena

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Errors in LGI command
by 笹林大樹 28 Nov '23

28 Nov '23

External Email - Use Caution Dear Freesurfer experts, I have run the following command: recon-all -s sub-1001 -localGI -no-isrunning However, I got the error message as below. >> Warning: Input argument must be a character vector. > In ver (line 41) In freesurfer_read_surf (line 70) In find_corresponding_center_FSformat (line 26) Error using fprintf Function is not defined for 'struct' inputs. Error in freesurfer_read_surf (line 70) fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15)); Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); >> ERROR: find_corresponding_center_FSformat did not complete successfully! Linux dn003 3.10.0-1160.88.1.el7.x86_64 #1 SMP Tue Mar 7 15:41:52 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-1001 exited with ERRORS at Wed Nov 22 14:59:33 EST 2023 How can I resolve the problem? Thank you for your consideration. Best, Daiki Sasabayashi

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FreeSurfer Parcellation Using Glasser's Atlas (HCP-MMP1)
by Boa Sorte Silva, Narlon 28 Nov '23

28 Nov '23

Hi there, I am hoping to extract cortical thickness and volume data from FreeSurfer-processed subjects using the HCP-MMP1 atlas (Glasser et al 2016 Nature). I have found many discussions in the email list but I wasn’t able to understand whether this procedure can be reliably done using .annot files. I have found ?h.HCPMMP1.annot files online (e.g., ggsegGlasser: https://secure-web.cisco.com/1RCrRYR2kfqIYN7pxC6sGgF_XvdqzAAephS3DadIADfMm-…) in fsaverage space, which I have resampled to the subject’s space using mri_surf2surf as follows: # Apply Glasser’s 2016 HCP-MMIP1.0 atlas mri_surf2surf \ --hemi ${hemi} \ --srcsubject fsaverage \ --trgsubject ${id} \ --sval-annot fsaverage/label/${hemi}.HCPMMP1.annot \ --tval ${SUBJECTS_DIR}/${id}/label/${hemi}.HCPMMP1.annot Then I extracted the stats using this command: # Extract Thickness and Volume stats mris_anatomical_stats \ -a ${SUBJECTS_DIR}/${id}/label/${hemi}.HCPMMP1.annot \ -f ${SUBJECTS_DIR}/${id}/stats/${hemi}.HCPMMP1.stats \ -b ${id} ${hemi} My question is whether the output from this procedure can be reliably used as an accurate version of the HCP-MMP1 parcellated regions in the subject’s native space OR whether a more involved process is needed to generate the parcellation. Thank you for your help Best regards, Nárlon Cássio Nárlon C Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/CLEAR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon External Email - Use Caution

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Fwd: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label
by Suman Saha 28 Nov '23

28 Nov '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recon-all command, but I get the following error when I run the "recon-all -i sub.mgz -s sub1 -all" command: ERROR: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label Linux cbdl 6.2.0-37-generic #38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 2 18:01:13 UTC 2 x86_64 x86_64 x86_64 GNU/Linux recon-all -s my_sub exited with ERRORS at Fri Nov 24 23:43:39 IST 2023 Does anyone have any thoughts on how to trouble-shoot this one? I've attached the recon-all.log. 1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 22.04.1 3) recon-all.log: see attached 4) recon-all.error : see attached ---------- Forwarded message --------- From: Suman Saha <ecesuman06(a)gmail.com> Date: Sat, Nov 25, 2023 at 8:17 AM Subject: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label To: <freesurfer(a)nmr.mgh.harvard.edu> Hello FreeSurfer Developers, I'm attempting to run recon-all command, but I get the following error when I run the "recon-all -i sub.mgz -s sub1 -all" command: ERROR: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label Linux cbdl 6.2.0-37-generic #38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 2 18:01:13 UTC 2 x86_64 x86_64 x86_64 GNU/Linux recon-all -s my_sub exited with ERRORS at Fri Nov 24 23:43:39 IST 2023 Does anyone have any thoughts on how to trouble-shoot this one? I've attached the recon-all.log. 1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 22.04.1 3) recon-all.log: see attached 4) recon-all.error : see attached

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Longitudinal LME matlab error - Matrix singular or badly scaled
by Sophie Matis 28 Nov '23

28 Nov '23

External Email - Use Caution Hello FreeSurfer experts! I have carried out some analysis of changes in cortical thickness over time using the LME Matlab (R23b) Toolbox distributed within Freesurfer (7.4.1) in line with the instructions on this page: https://secure-web.cisco.com/1T0jceJqjr8o0YltVDmmB4EAlEhKr0pMp8gIavJ6vaUX1H… At this stage I just want to look at changes over time within each of three groups. For two groups I have been able to proceed through the steps fine and have my significance files which look normal. For the last group I am running into an error on the "[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3); " step. MATLAB returns "Warning: Matrix is singular, close to singular or badly scaled" and lhTh0 and lhRe are created as matrices with only NaN values. Has anyone run into this error before or have any tips for troubleshooting it? I haven't had any errors on the longitudinal processing steps and visual QC on my files looks normal. No errors on mris_preproc or mri_surf2surf. An aparcstats2table for thickness doesn't reveal any NaNs. My design matrix is created with X = [ones(length(M),1) M] after following the suggested sortData code from the wiki Contrast is [0 1] This is my qdec file: fsid fsid-base yearsfromBL 108_MR1 108 0.00 199_MR1 199 0.00 199_MR2 199 1.10 199_MR3 199 2.25 202_MR1 202 0.00 204_MR1 204 0.00 204_MR2 204 1.16 204_MR3 204 2.30 223_MR1 223 0.00 0821_MR1 0821 0.00 0931_MR1 0931 0.00 1010_MR1 1010 0.00 1010_MR2 1010 1.84 1031_MR1 1031 0.00 1031_MR2 1031 1.00 1031_MR3 1031 2.13 1064_MR1 1064 0.00 1064_MR2 1064 2.01 1125_MR1 1125 0.00 1134_MR1 1134 0.00 1134_MR2 1134 1.17 1134_MR3 1134 2.28 1233_MR1 1233 0.00 1233_MR2 1233 1.05 1373_MR1 1373 0.00 1439_MR1 1439 0.00 1439_MR2 1439 1.14 1439_MR3 1439 2.28 1475_MR1 1475 0.00 1475_MR2 1475 1.04 1475_MR3 1475 2.03 1522_MR1 1522 0.00 1522_MR2 1522 2.07 1541_MR1 1541 0.00 1541_MR2 1541 1.47 1551_MR1 1551 0.00 1551_MR2 1551 0.98 1551_MR3 1551 2.05 1572_MR1 1572 0.00 1572_MR2 1572 1.03 1625_MR1 1625 0.00 1625_MR2 1625 1.06 1637_MR1 1637 0.00 1641_MR1 1641 0.00 1656_MR1 1656 0.00 1656_MR2 1656 0.94 1656_MR3 1656 2.26 1755_MR1 1755 0.00 1755_MR2 1755 1.04 1755_MR3 1755 2.01 1829_MR1 1829 0.00 09154_MR1 09154 0.00 09154_MR2 09154 1.01 09154_MR3 09154 2.01 12110_MR1 12110 0.00 12110_MR2 12110 1.04 Any help appreciated! Thank you, Sophie Matis | Data Management & Research Officer School of Health Sciences & Brain and Mind Centre Faculty of Medicine and Health The University of Sydney Brain and Mind Centre, 94-100 Mallett Street, Camperdown (M02G) | The University of Sydney | NSW | 06 sophie.matis(a)sydney.edu.au<mailto:shona.brinley@sydney.edu.au> | sydney.edu.au<http://secure-web.cisco.com/1TuWK5WUev2Fb_3Y4GMAFPyrgRjl5K2o4Isb-heH5rrBUMM…> CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this email if necessary.

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Fwd: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label
by Suman Saha 27 Nov '23

27 Nov '23

External Email - Use Caution Regards, *Suman Saha* ---------- Forwarded message --------- From: Suman Saha <ecesuman06(a)gmail.com> Date: Sat, Nov 25, 2023 at 8:21 AM Subject: Fwd: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label To: <freesurfer(a)nmr.mgh.harvard.edu> Regards, *Suman Saha* ---------- Forwarded message --------- From: <freesurfer-owner(a)nmr.mgh.harvard.edu> Date: Sat, Nov 25, 2023 at 8:18 AM Subject: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label To: <ecesuman06(a)gmail.com> You are not subscribed to this mailing list, and your message has been automatically rejected. Please subscribe to the list following the instructions at: https://secure-web.cisco.com/1GUd1hdBRPxgF-mL_r8NbneNA4m_Qy5_5__TuOpcP6Rr01… IMPORTANT: Make sure you are sending your message using the same email address that was used to subscribe to the list! Further, registering for a FreeSurfer license does not mean you have been subscribed to the list! If you think that your messages are being rejected in error, contact the mailing list owner at freesurfer-owner(a)nmr.mgh.harvard.edu ---------- Forwarded message ---------- From: Suman Saha <ecesuman06(a)gmail.com> To: freesurfer(a)nmr.mgh.harvard.edu Cc: Bcc: Date: Sat, 25 Nov 2023 08:17:35 +0530 Subject: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recon-all command, but I get the following error when I run the "recon-all -i sub.mgz -s sub1 -all" command: ERROR: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label Linux cbdl 6.2.0-37-generic #38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 2 18:01:13 UTC 2 x86_64 x86_64 x86_64 GNU/Linux recon-all -s my_sub exited with ERRORS at Fri Nov 24 23:43:39 IST 2023 Does anyone have any thoughts on how to trouble-shoot this one? I've attached the recon-all.log. 1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 22.04.1 3) recon-all.log: see attached 4) recon-all.error : see attached

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Re: [Freesurfer] recon-all error - MRISlabel2Mask()
by Mark Wagshul 27 Nov '23

27 Nov '23

External Email - Use Caution Here is the log file, thanks for the help! Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately. -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Wednesday, November 22, 2023 1:22 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 237, Issue 26 CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the "Phish Alert" button on the top right of the Outlook dashboard to report any suspicious emails. Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1rJkZ5uxySrpWhsLGjGTDASTPuao4nugI2v8ucy4w4t46S… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Help (Xincen Wu) 2. Re: freesurfer results QC (yunus soleymani) 3. Unable to add FGATIR during thalamic segmentation (Pal, Amrita) 4. issue with mri_vol2surf (Atena Akbari) 5. Re: Unable to add FGATIR during thalamic segmentation (Iglesias Gonzalez, Juan E.) 6. Re: run recon-all with already skull-stripped data (Douglas N. Greve) 7. Re: total intracranial volume (Douglas N. Greve) 8. Re: Fwd: About Mean LGI value (Douglas N. Greve) 9. Re: Transformation of volume images (Douglas N. Greve) 10. Re: Distance Measurement After recon-all (Douglas N. Greve) 11. Re: recon-all error - MRISlabel2Mask() (Douglas N. Greve) 12. Re: Boundary based registration on partial FoV to MNI space (Douglas N. Greve) 13. Re: Errors in recon-all command (Douglas N. Greve) ---------------------------------------------------------------------- Message: 1 Date: Wed, 22 Nov 2023 08:44:18 -0500 From: Xincen Wu <xlwu25(a)groton.org> Subject: [Freesurfer] Help To: Freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CADAiWu4jbXuW22WA9OWD5E0sdrXA9ZJw5Eo-K+z3y7s0CsPRNA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi, I am using freesurfer. I have gone through with the installation and diagnostics and everything works fine. FOr example, using the command recon-all --help in terminal yields a bunch of directions. Yet, when I enter something like: recon-all -s bert -autorecon1 an error pops up saying my python3 is problematic. However, I regularly use python3 and redownloaded it after. Please advise on the issue at hand. Thanks, Lucas

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Functional data analysis with longitudinal data
by Akkoyunlu, Beyza 26 Nov '23

26 Nov '23

External Email - Use Caution Hi, I am doing a longitudinal experiment and I already run the longitudinal anatomical pipeline. I am not sure which anatomical data I should register my functional data to? My first idea was to use base anatomical image, but when I checked results I realised that the white gray matter boundaries are not so good with the subject’s base. Do you have a suggestion whether I should use subject’s base data or base.long.post data? FYI, we are using MEMPRAGE as our anatomical pipeline. Thanks Best, Beyza

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