Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30076 discussions

Hippocampal subfield data
by Taylor, Lisa 10 Dec '21

10 Dec '21

External Email - Use Caution Hi, Any reason why my participant is not creating hippocampal subfield data? Thank you Lisa ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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Fieldmap Images in Nifti Format
by Kaplan, Elizabeth 10 Dec '21

10 Dec '21

External Email - Use Caution Hi All, I am working on processing diffusion data with Tracula and am running into an error when attempting to use fieldmaps to compensate for B0 inhomogeneity distortions. The error that I run into reads "ERROR: must specify as many gradient vector tables as DWI scans ". I am able to completely run Tracula processing when specifying dob0 = 0. Is it possible to use fieldmap images that are in Nifti format or is DICOM format required for this input? Any other guidance is greatly appreciated!

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PhD position
by Dídac Vidal 10 Dec '21

10 Dec '21

External Email - Use Caution At the Center for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have an available PhD fellowship for a candidate highly interested in applying longitudinal, multimodal models on neuroimaging data and its relation to genetics and cognition to understand the brain foundations for episodic memory preservation and loss in older age The application deadline is: 16.01.2022 Please see more info here: https://secure-web.cisco.com/1wnEXnVTSaJxvqRbBY18QbYibaL9-BHWSM5gMKGsdW_VLE… P.S. Interested candidates are welcome to contact Didac Vidal-Pineiro ( d.v.pineiro(a)psykologi.uio.no) All the best, Dídac -- Dídac Vidal Piñeiro

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Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file
by fsbuild 09 Dec '21

09 Dec '21

External Email - Use Caution Hello Jürgen, Try running the bash shell from the terminal, e.g., before running anything type, $ bash - and then try your command again. If that works then I would set your login shell to bash (as the default is dash). - R. On Dec 7, 2021, at 01:46, juergen.haenggi(a)upd.unibe.ch wrote:        External Email - Use Caution        Dear Anastasiathank a lot for the answer.We use Ubuntu 18.04..6 LTS.When we run the command directly in the terminalbedpostx_mgh -n 2 -model 1 /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmriwe get the sane error/usr/local/freesurfer/bin/bedpostx_mgh: 128: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(„ unexpectedwhen we run the command you sent in your last email, i.e. fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g’`)we get the following errorBadly placed ()’s.Thanks in advanceRegardsJürgenAm 03.12.2021 um 00:02 schrieb Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:Hi Jürgen - I haven't been able to replicate your error locally. What operating system are you running it on? And what do you see if you try run the line that errors out directly on the command line? The line is:fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g'`)Thanks,Anastasia.From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.ch>Sent: Thursday, November 25, 2021 1:40 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file         External Email - Use Caution        Dear Anastasiacat $FSLDIR/etc/fslversion reported6.0.5.1:57b01774I guess its the newest version availableThanksJürgenAm 24.11.2021 um 15:53 schrieb Yendiki, Anastasia <AYENDIKI@MGH.HARVARD.EDU>:Hi Jürgen - Can you check what's in this file: $FSLDIR/etc/fslversion ?Thanks,Anastasia.From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.ch>Sent: Wednesday, November 24, 2021 12:53 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file         External Email - Use Caution        Dear Anastasiawhen I type $FSLDIR in the terminal, I get /usr/local/fsl: permission denied.this is the right path where fsl is installed.however, I can start FSL GUI and also other FSL commands.Best JürgenAm 24.11.2021 um 01:20 schrieb Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:Hi Jürgen - What's your $FSLDIR set to?Anastasia.From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.ch>Sent: Tuesday, November 23, 2021 9:36 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file         External Email - Use Caution        Dear Anastasiathank you for the new option. It works. Now we were able to finish trac-all -prep without any further problem.However, when we try to run trac-all -bedp, the following error occurred:----------trac-all -bedp -c /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example_DICOM_NIFTI_ANTs.txtINFO: SUBJECTS_DIR is /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjectsINFO: Diffusion root is /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720Actual FREESURFER_HOME /usr/local/freesurferln -sf .../dlabel/diff/aparc+aseg_mask.bbr.nii.gz /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/nodif_brain_mask.nii.gzWARN: Running bedbostx locally - this might take a whileWARN: It is recommended to run this step on a clusterbedpostx_mgh -n 2 -model 1 /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/usr/local/freesurfer/bin/bedpostx_mgh: 128: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected——————we have found this message from 2014 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/18T9Slnh9GWxjhAdkDbh-RBVdxl_EEto9Zyi1R… it meanwhile possible to run bedpostx_mgh also locally or do we have to run bedpostx directly as suggested in the link?BestJürgenAm 23.11.2021 um 01:14 schrieb Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:Ah yes, I did say that this would be feasible in 7..2, before 7.2 came out �� One more bug fix, in the same place (and then in the dev version):MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1CVaoIFDW7Y1gTCajFc6xesbgRXEyFbVCo4eNH… now on the dTE from the config file will supersede the one from the DICOM header. Thanks for finding this and let us know if there are any other issues.Anastasia.From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.ch>Sent: Monday, November 22, 2021 4:47 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file         External Email - Use Caution        Dear Anastasiathank you for providing the bug fix. It works and solved our problem.However, another (old) problem occurred wrt the field map for which we did not find any solution yet:---------------------------------------------------------writing to /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0pha.nii.gz...mri_probedicom --i /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm > /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0info.datERROR: Need dTE for field map /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcmLinux upd-159253 4.15.0-162-lowlatency #170-Ubuntu SMP PREEMPT Mon Oct 18 13:19:21 UTC 2021 x86_64 x86_64 x86_64 GNU/Linuxtrac-preproc exited with ERRORS at Mon Nov 22 09:18:01 CET 2021-----------------------------------------------------------For some reasons, dTE cannot be extracted from the b0info.dat file (see attachment).. Indeed, there is only one echo time entry (EchoTime 7.38) in the b0info.dat file maybe due to the fact that there is also only one echo time entry (EchoTime 7.38) in the DICOM header.Specifying dTE = 2.46 in the config file does not solve the problem, neither with NIFTI nor DICOM file format for the field map.In a former email, you mentioned that this should be possible.The log and config file are also attached.Is there any work around for this problem?Thanks in advanceBest,JürgenAm 20.11.2021 um 18:11 schrieb Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:Hi Jürgen - You have diagnosed the problem correctly. It's specific to the case when you have 1 DWI run only. I committed a bug fix for this. For now you can get it from here (and it should get merged into the dev version in a couple of days):MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/129BVv4E3jHc7-9Fa7JjFOZHaSkWycuz_pfP1F… you please save this version of trac-preproc to your $FREESURFER_HOME/bin/ and tell us if it fixes the problem? Thank you for bringing this to our attention.Best,Anastasia.From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.ch>Sent: Wednesday, October 27, 2021 8:19 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file         External Email - Use Caution        Dear TRACULA expertsI try to run TRACULA FS7.2 on a Linux machine and get the following error (see below). A similar problem has already been reported in the archives, but I found no solution.MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Xuw41tWbmnuzmqIIpQYcNE6gW2n7sh1D2Q0ej… the file "dwi_orig_las.1.bvals“ was renamed to „dwi_orig_las.bvals“  earlier in the runmv -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvalsit cannot be found by awk and as a result, I guess, the index.txt file is empty and therefore eddy_openmp terminated.How can I fix this problem?The terminal output, log and config files are attached.Thank you for any advise in advanceRegardsJürgen—————— error ————awk: fatal: cannot open file `/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals' for reading (No such file or directory)eddy_openmp --imain=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz --mask=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs --bvals=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals --acqp=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/acqp.txt --index=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt --data_is_shelled --out=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwiEddyInputError:  Error when attempting to read --index file /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txtTerminating programLinux upd-159253 4.15.0-147-lowlatency #151-Ubuntu SMP PREEMPT Fri Jun 18 20:06:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linuxtrac-preproc exited with ERRORS at Wed Oct 27 13:41:49 CEST 2021upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test>——————_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PPWJNNIefyUZcs5AKLAKws2SzfUSFKBgSB9_C… information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1hBCrgCuLzX5l1PYV8M7sW_m5xxNQPHaSPIQ_LG… If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PPWJNNIefyUZcs5AKLAKws2SzfUSFKBgSB9_C… information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1hBCrgCuLzX5l1PYV8M7sW_m5xxNQPHaSPIQ_LG… If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PPWJNNIefyUZcs5AKLAKws2SzfUSFKBgSB9_C… information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1hBCrgCuLzX5l1PYV8M7sW_m5xxNQPHaSPIQ_LG… If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PPWJNNIefyUZcs5AKLAKws2SzfUSFKBgSB9_C… information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1hBCrgCuLzX5l1PYV8M7sW_m5xxNQPHaSPIQ_LG… If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PPWJNNIefyUZcs5AKLAKws2SzfUSFKBgSB9_C… information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1hBCrgCuLzX5l1PYV8M7sW_m5xxNQPHaSPIQ_LG… If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file
by fsbuild 09 Dec '21

09 Dec '21

External Email - Use Caution Sorry, I should have said you need to directly invoke the script with bash, $ bash bedpostx_mgh -n 2 -model 1 <all other args> Alternately, if you can edit the script, then change the first line from:#!/bin/shto:#!/usr/bin/env bash and you should not need to preface it with bash from the command line. - R. On Dec 9, 2021, at 03:01, juergen.haenggi(a)upd.unibe.ch wrote:        External Email - Use Caution        Dear expertthanks a lot for your suggestion.the error initially occurred using tcsh.if I use bash as you suggested, the same error is reported./usr/local/freesurfer/bin/bedpostx_mgh: 128: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(„ unexpectedwrt the command fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g’`), the message "Badly placed ()’s.“ disappears when using bash instead of tcsh, but no output is produced. I do not understand for what purpose I have to run this command and what output, if any, should be expected.Any idea how to get bedpostx_mgh working is highly appreciated?Thanks in advanceRegardsJürgenAm 08.12.2021 um 18:25 schrieb fsbuild <fsbuild@contbay.com>:Hello Jürgen,Try running the bash shell from the terminal, e.g., before running anything type,$ bash- and then try your command again.If that works then I would set your login shell to bash (as the default is dash).- R.On Dec 7, 2021, at 01:46, juergen.haenggi@upd.unibe.ch wrote:        External Email - Use Caution        Dear Anastasiathank a lot for the answer.We use Ubuntu 18.04.6 LTS.When we run the command directly in the terminalbedpostx_mgh -n 2 -model 1 /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmriwe get the sane error/usr/local/freesurfer/bin/bedpostx_mgh: 128: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(„ unexpectedwhen we run the command you sent in your last email, i.e. fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g’`)we get the following errorBadly placed ()’s.Thanks in advanceRegardsJürgenAm 03.12.2021 um 00:02 schrieb Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:Hi Jürgen - I haven't been able to replicate your error locally. What operating system are you running it on? And what do you see if you try run the line that errors out directly on the command line? The line is:fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g'`)Thanks,Anastasia.From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.ch>Sent: Thursday, November 25, 2021 1:40 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh..harvard.edu>Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file         External Email - Use Caution        Dear Anastasiacat $FSLDIR/etc/fslversion reported6.0.5.1:57b01774I guess its the newest version availableThanksJürgenAm 24.11.2021 um 15:53 schrieb Yendiki, Anastasia <AYENDIKI@MGH.HARVARD.EDU>:Hi Jürgen - Can you check what's in this file: $FSLDIR/etc/fslversion ?Thanks,Anastasia.From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd..unibe.ch <juergen.haenggi@upd.unibe.ch>Sent: Wednesday, November 24, 2021 12:53 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file         External Email - Use Caution        Dear Anastasiawhen I type $FSLDIR in the terminal, I get /usr/local/fsl: permission denied.this is the right path where fsl is installed.however, I can start FSL GUI and also other FSL commands.Best JürgenAm 24.11.2021 um 01:20 schrieb Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:Hi Jürgen - What's your $FSLDIR set to?Anastasia.From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.ch>Sent: Tuesday, November 23, 2021 9:36 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file         External Email - Use Caution        Dear Anastasiathank you for the new option. It works. Now we were able to finish trac-all -prep without any further problem.However, when we try to run trac-all -bedp, the following error occurred:----------trac-all -bedp -c /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example_DICOM_NIFTI_ANTs.txtINFO: SUBJECTS_DIR is /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjectsINFO: Diffusion root is /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720Actual FREESURFER_HOME /usr/local/freesurferln -sf ../dlabel/diff/aparc+aseg_mask.bbr..nii.gz /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/nodif_brain_mask.nii.gzWARN: Running bedbostx locally - this might take a whileWARN: It is recommended to run this step on a clusterbedpostx_mgh -n 2 -model 1 /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/usr/local/freesurfer/bin/bedpostx_mgh: 128: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected——————we have found this message from 2014 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PZw3Rw8y7Owkru69l62f3qrEeHiVBpRsvZg7R… it meanwhile possible to run bedpostx_mgh also locally or do we have to run bedpostx directly as suggested in the link?BestJürgenAm 23.11.2021 um 01:14 schrieb Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out �� One more bug fix, in the same place (and then in the dev version):MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1BcqFiy7b_RheZDW7Y6dSsECFm81wUqvpTrx6G… now on the dTE from the config file will supersede the one from the DICOM header. Thanks for finding this and let us know if there are any other issues.Anastasia.From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd..unibe.ch <juergen.haenggi@upd.unibe.ch>Sent: Monday, November 22, 2021 4:47 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file         External Email - Use Caution        Dear Anastasiathank you for providing the bug fix. It works and solved our problem.However, another (old) problem occurred wrt the field map for which we did not find any solution yet:---------------------------------------------------------writing to /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0pha.nii.gz...mri_probedicom --i /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm > /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0info.datERROR: Need dTE for field map /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcmLinux upd-159253 4.15.0-162-lowlatency #170-Ubuntu SMP PREEMPT Mon Oct 18 13:19:21 UTC 2021 x86_64 x86_64 x86_64 GNU/Linuxtrac-preproc exited with ERRORS at Mon Nov 22 09:18:01 CET 2021-----------------------------------------------------------For some reasons, dTE cannot be extracted from the b0info.dat file (see attachment). Indeed, there is only one echo time entry (EchoTime 7.38) in the b0info.dat file maybe due to the fact that there is also only one echo time entry (EchoTime 7.38) in the DICOM header.Specifying dTE = 2.46 in the config file does not solve the problem, neither with NIFTI nor DICOM file format for the field map.In a former email, you mentioned that this should be possible.The log and config file are also attached.Is there any work around for this problem?Thanks in advanceBest,JürgenAm 20.11.2021 um 18:11 schrieb Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:Hi Jürgen - You have diagnosed the problem correctly. It's specific to the case when you have 1 DWI run only. I committed a bug fix for this. For now you can get it from here (and it should get merged into the dev version in a couple of days):MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1vogQP6gWZ3A7n4EogQreDkBb-38S1C2taCJcr… you please save this version of trac-preproc to your $FREESURFER_HOME/bin/ and tell us if it fixes the problem? Thank you for bringing this to our attention.Best,Anastasia.From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.ch>Sent: Wednesday, October 27, 2021 8:19 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file         External Email - Use Caution        Dear TRACULA expertsI try to run TRACULA FS7.2 on a Linux machine and get the following error (see below). A similar problem has already been reported in the archives, but I found no solution.MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1kdXnIzyrqnSlUAKpjf6Ehu2NoR_fdE1tNkmf4… the file "dwi_orig_las.1.bvals“ was renamed to „dwi_orig_las.bvals“  earlier in the runmv -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvalsit cannot be found by awk and as a result, I guess, the index.txt file is empty and therefore eddy_openmp terminated..How can I fix this problem?The terminal output, log and config files are attached.Thank you for any advise in advanceRegardsJürgen—————— error ————awk: fatal: cannot open file `/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals' for reading (No such file or directory)eddy_openmp --imain=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz --mask=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs --bvals=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals --acqp=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/acqp.txt --index=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt --data_is_shelled --out=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwiEddyInputError:  Error when attempting to read --index file /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txtTerminating programLinux upd-159253 4.15.0-147-lowlatency #151-Ubuntu SMP PREEMPT Fri Jun 18 20:06:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linuxtrac-preproc exited with ERRORS at Wed Oct 27 13:41:49 CEST 2021upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test>——————_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1s2hfIaO8Fd-4kPJit80Ioh7TPfSykIu_rzSPD… information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1AAfp-_alHB0TRruMwtGnwwgSfdBuy0Jaw1vM1x… If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.. _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1s2hfIaO8Fd-4kPJit80Ioh7TPfSykIu_rzSPD… information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1AAfp-_alHB0TRruMwtGnwwgSfdBuy0Jaw1vM1x… If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1s2hfIaO8Fd-4kPJit80Ioh7TPfSykIu_rzSPD… information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1AAfp-_alHB0TRruMwtGnwwgSfdBuy0Jaw1vM1x… If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1s2hfIaO8Fd-4kPJit80Ioh7TPfSykIu_rzSPD… information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1AAfp-_alHB0TRruMwtGnwwgSfdBuy0Jaw1vM1x… If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.. _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1s2hfIaO8Fd-4kPJit80Ioh7TPfSykIu_rzSPD… information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1AAfp-_alHB0TRruMwtGnwwgSfdBuy0Jaw1vM1x… If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FREESURFER
by Alison McDonnell 09 Dec '21

09 Dec '21

External Email - Use Caution Hi all, I'm trying to use mris_convert and can't get it to work. current command I'm using: mris_convert lh.full.flat.patch.3D lh.full.flat.patch.3D.asc also can't seem to find the difference between mris convert and mri convert so don't know if I should be using that instead. any advice would be appreciated thanks, Ali

2 4

auto-configure TRACULA for BIDS data
by Yendiki, Anastasia 08 Dec '21

08 Dec '21

Dear FreeSurfers - There's a new script in the development version called dmri_bids_config. You can get it here: https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/dmri_bi… There is documentation here: https://surfer.nmr.mgh.harvard.edu/fswiki/dmri_bids_config It will parse the BIDS directory structure, find all the DWI scans (and field maps, if any), and generate the TRACULA configuration file for you. With this file, you can then run TRACULA to pre-process the DWIs and reconstruct tracts of interest. As an added bonus, it will also generate an FSGD file, based on the participants.tsv file in your input BIDS directory. The FSGD file can be used for stats with mri_glmfit. It'd be great to have people test this script on their BIDS datasets and report any issues. Both legacy and newer data welcome! Thanks, Anastasia.

1 0

Propagating hippocampal subfield segmentation to native T2w space
by Eyre, Michael 08 Dec '21

08 Dec '21

External Email - Use Caution Hi all Regarding hippocampal subfield segmentation in FS7- how can I move the segmentation result to native T2w space? I plan to compare the result with a manual segmentation which was done in this space, using scripts which require nifti inputs. I have run FS7 specifying with the -cm flag that this takes place in my T1 (MP2RAGE) 0.65mm isotropic resolution: recon-all -all -s <subject> -i T1w.nii -T2 T2w.nii -T2pial -gcut -cm Then I ran the Hc subfield segmentation, specifying that my T2w volume (3D-SPACE, 0.55mm isotropic) should be used for this: segmentHA_T2.sh <subject> T2w.nii 3DT2 0 The output that I want to move back to native 3DT2 space is the labelled volume lh.hippoAmygLabels-3DT2.v21.mgz (or the nifti of this which of course I can create using mri_convert). However this volume is 0.333mm isotropic and has a limited field of view - from the documentation: "Note that [lr]h.hippoAmygLabels-T1.v21.mgz and [lr]h.hippoAmygLabels-T1.v21.[hierarchy].mgz cover only a patch around the hippocampus, at a higher resolution than the input image." The most relevant guidance I can find in the documentation is "[lr]h.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz live in the same voxel space as the other Freesurfer volumes (e.g., orig.mgz, nu.mgz, aseg.mgz), so you can use it directly to produce masks for further analyses, but its resolution is lower (1 mm vs 0.333 mm)." In my case FSvoxelSpace is at 0.65mm resolution, but this is still lower than my T2w volume (0.55mm) and so would involve some downsampling (0.333mm --> 0.65mm --> 0.55mm) which I would like to avoid. I have tried various linear registration approaches but I always end up with a result which, although in 0.55mm space, is clearly not aligned with the hippocampus when viewed together with my T2w.nii in ITK-SNAP. Any suggestions would be much appreciated! Many thanks Mike

2 2

Hippocampal Subfield data not populating
by Taylor, Lisa 08 Dec '21

08 Dec '21

External Email - Use Caution Hi, Sorry if this email has been seen. I got an automatic response that my previous emails were in the queue waiting to be approved due to the email size, but haven't seen an approval yet. So, I am trying again without the email attachments (both recon all and hippocampal subfield log files) to see if it might be more efficient this way. Running the hippocampal-subfields-T1 argument for some reason is not populating the data I need. My recon-all log says it was exited without error, and my hippocampal subfield log file seems to have run smoothly except for this one line that I am not sure is telling or not: /data/opt/apps/freesurfer/6.0.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 46: 2066 Killed "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args Please advise! Thank you. Lisa ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

2 2

InfantFS - resampling asset to native space
by Fateme Haghpanah 08 Dec '21

08 Dec '21

External Email - Use Caution Dear FreeSurfer Developers, We are using InfantFS and noticed that after running recon-all ("infant_recon_all --newborn --s ${SUBJ}”) , the voxel size changes to 1*1*1. I know that using "mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz” we can convert the aseg output of adult FreeSurfer to native space. Is there any similar command to do so for infants? I wanted to try this one, however there is no rawavg.mgz file in the mri folder of infant subjects. Thanks in advance, Fateme

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