Freesurfer November 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
117 discussions

Converting register.dat file to reg.lta
by Mirsol Choi 30 Nov '23

30 Nov '23

External Email - Use Caution Hello there, I am wondering if there is a way to convert register.dat file produced from dt_recon to reg.lta. I need a reg.lta file that contains registration between the DTI data and processed (recon-all) T1 data. I have tried to perform bbregister, but the alignment is completely off. Thank you so much for your time! Mirsol

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Calculating LGI with existing masks
by Ding, Yan 29 Nov '23

29 Nov '23

External Email - Use Caution Hi, I am new to FreeSurfer. And I have a question regarding the calculation of the local gyrification index (LGI). I have one brain MRI image and I have manually created the mask of the cortex. Instead of calculating the LGI from scratch with the recon-all command, I want to do it using the mask I created. How should I do it? Thank you very much in advance. Best, Ryan

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Group Analysis - 4 groups 3 covariates
by Tejaswi D. Sudhakar 29 Nov '23

29 Nov '23

External Email - Use Caution Hi, I would like to run a group analysis on 4 groups (patientM, patientF, controlM, controlF) with 3 covariates (age, cogscore1, cogscore2). I am running with dods - so I would have 16 total regressors. How would I create contrast matrices for this? I have this so far: 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 Secondly, I created lh.train.thickness.10B.mgh since the initial run was not qcached. How can I check if there is an error with this file? Thanks in advance.

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trac-all -paths Abort ERROR
by Lauren Stephens 29 Nov '23

29 Nov '23

External Email - Use Caution Hi FreeSurfers, I have been running Tracula on a two time point longitudinal data set. I have successfully ran 95% of my data all the way through -stat. However, with 7 of my subjects trac-all -path runs for about 24 hours and then gives the following error: Running MCMC burn-in jumps Running MCMC main jumps Abort Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version 22.6.0: Wed Oct 4 21:25:26 PDT 2023; root:xnu-8796.141.3.701.17~4/RELEASE_X86_64 x86_64 trac-paths exited with ERRORS at Tue Nov 28 19:25:34 PST 2023 There is no record of this error occurring in the trac-all log and there is no trac-paths showing in the scripts folder. ANy suggestions on why this is occurring and how to fix it? I am using an iMac Pro running Ventura 13.6.1 and FreeSurfer Version 7.3.2. Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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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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Freesurfer November 2023