Freesurfer April 2021

freesurfer@nmr.mgh.harvard.edu

104 participants
144 discussions

Longitudinal processing: QA
by Malo Gaubert 19 Apr '21

19 Apr '21

External Email - Use Caution Hello FreeSurfer developers, I am trying to apply longitudinal processing on T1w MRI data for two timepoints (~8 months between the two TP) in adolescents in order to perform vertex-based analyses. I am following the online tutorial here for the preprocessing: https://secure-web.cisco.com/1AR-A4eBY63Zb7ogV-L0wed0Mf63cN1cf9Evvcu56pwG2m… Thus I launched the creation of BASE followed by the LONGITUDINAL. Everything went well for recon-all for these 3 steps. Now, I want to do the QA on the data and I have two questions regarding this QA: 1/ For one subject, for the two timepoints, the white and pial surface are entering in the left lateral ventricle as displayed in figure 1 below (session 1 of the subject; cross-sectional), while the aseg is fine (this area is considered as Lateral ventricle, see figure 2, see below). What correction could I apply for this case ? 2/ For some subjects, there is a small shift between the pial of the two sessions (or the white; see figure 3 (see below)=display of the norm of my norm and pial/white for the two timepoints (long)) and/or some weird/non straight/zigzag lines for pial or white (see figure 3, especially between temporal pole and the rest of the brain). What could be the problem in this case? Could it be related to some bad quality of T1w images? 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0.tar.gz 2) Platform: Ubuntu 18 (Virtual Machine on remote server) 3) uname -a: Linux ubuntu18-cbrain-042020 4.15.0-135-generic #139-Ubuntu SMP Mon Jan 18 17:38:24 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Any help would be appreciated. Best regards, Malo Link to figure 1: https://secure-web.cisco.com/1Z0OIVNfAyd0P4dX5TvUfticgFxyac5XLFP9qZ15LY2KoH… Link to figure2: https://secure-web.cisco.com/1dkQLGxh5x41ISY3MzCyMUowvQmrn9m-TXAqgZfq29hFI5… Link to figure3: https://secure-web.cisco.com/1Nqbq7hapdkZjMI0hXAMBIcoKgeG0dkh3UzuuOGbjE_sUP…

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Talairach Failed: Distorted T1
by Harkey, Thomas Jarrott 18 Apr '21

18 Apr '21

External Email - Use Caution Hello, My name is Thomas Harkey and I am conducting research using FreeSurfer. After running recon-all on this patient, the Talairach failed according to the .log file. No stats were calculated but loading the orig.mgz file into FreeView looks like this (see image attached). This DICOM file was successfully uploaded into other programs. How can I fix this error? Kind regards, -- Thomas Harkey University of Arkansas for Medical Sciences College of Medicine, Class of 2022 501-553-6318 TJHarkey(a)uams.edu<mailto:TJHarkey@uams.edu> ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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glmfit with aseg table: view surface overlay
by Griem, Julia 18 Apr '21

18 Apr '21

External Email - Use Caution Dear Freesurfer team, I am comparing subcortical volumes (aseg table) in 2 groups with no other variables. Based on the GLM lecture slides from the course I attended, I ran the following glmfit command: mri_glmfit --table aseg_table.txt --fsgd FSGD/DemographicsSubcortBinaryGroup.fsgd --C Contrasts/HC-ASPD.mtx --C Contrasts/ASPD-HC.mtx --glmdir roi.binarygroup.glmdir It created all the correct output and subdirectories. I then used freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=ASPD-HC/sig.mgh but an error saying "failed to load surface overlay" comes up and the terminal error message is "number of vertices in overlay data does not match with surface". I assume this is because I am trying to load a 'whole-brain' sig.mgh onto a lh surface? Do I have to change the glmfit command to specify hemispheres, and if so, how do I do that since I do not want to look at cortical but subcortical data? Or alternatively, can I load both hemispheres into freeview so the overlay sig.mgh fits? Thank you so much, Julia

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Re: [Freesurfer] Running recon-all with FLAIR
by Edina Szabó 18 Apr '21

18 Apr '21

External Email - Use Caution Hi Douglas, Thank you for your response! I really appreciate it. I ran the command – it works if I replace --i with --mov. How can I use the new FLAIRraw.lta to create a new FLAIR-based pial surface? For example, should I run recon-all -autorecon2 or some later step? Also, we were assuming that registration of the FLAIR to the T1 was the problem (underestimated pial surface), since the FLAIR.mgz produced by Freesurfer was not well registered to the T1.mgz. So, if that's the case, and I have another well-registered FLAIR (using FSL or SPM), is there a way to skip the Freesurfer registration and use that FLAIR to create the FLAIR pial surface? Thank you for your help in advance! All the best, Edina Szabo __ Edina Szabo, PhD Research Fellow Department of Anesthesiology, Critical Care and Pain Medicine Boston Children's Hospital | Harvard Medical School ----------------- Try this cd subject/mri mri_coreg --i orig/T2raw.mgz --targ orig.mgz --reg transforms/T2raw.lta You can run with multiple threads by adding --threads N where N is the number of threads On 3/29/2021 5:18 PM, Edina Szabó wrote: External Email - Use Caution Dear All, We are running recon-all on the latest version of FreeSurfer (v7.1.1). We are using both T1 and FLAIR images to better define the pial surfaces, but when we run the recommended command line (recon-all -subject subjectname -i /path/to/input_volume -FLAIR /path/to/FLAIR_volume -FLAIRpial -all) the pial surface is very underestimated (?.pial.FLAIR – and the aseg volume is based on these surfaces), and we get better results without the FLAIR. It seems that FreeSurfer mis-registers the FLAIR to the T1 during the process. Is there a separate step we should do to register FLAIR to T1? Thank you, Edina _______________________________________________ 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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Re: [Freesurfer] mris_average_surface fails
by fsbuild 18 Apr '21

18 Apr '21

External Email - Use Caution Hello Mudathir, Your account needs admin/sudo privileges in order to write files under /Applications.  If you made the first account on the machine when it was new and powered up after taking it out of the box, then at the terminal all you should need to do is preface commands with “sudo”.  If you use the Finder, then it will ask you to authenticate via a popup window, e.g., when installing software.  Once you authenticate via the terminal or via the Finder window and the system accepts your password, then by default your admin permissions will be cached for a certain period of time. One way to test that is to open a terminal window and do, $ sudo touch /Applications foo<output deleted>Password: If that succeeds, then you should be able to remove the file w/o typing sudo while your credentials are still cached,$ rm /Applications/foo With admin/sudo privileges, the 7.1..1 Mac package installer program,https://secure-web.cisco.com/1xtJzx0lQIrKf7ZCl0ntd1jilGKonbJiHvRDb7… - can be used to install the freesurfer 7.1.1 distribution under /Applications/freesurfer/7.1.1.  The freesurfer 6 or freesurfer 7 *.pkg files should set all the permissions to be correct on the freesurfer files. You can re-home SUBJECTS_DIR in the shell environment (this example assumes the pkg file installed it as /Applications/freesurfer/7.1.1) $ bash$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.1.1 FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjects MNI_DIR           /Applications/freesurfer/7..1.1/mni You can change the setting of SUBJECTS_DIR to point to a directory where you always have write permission (do not need to authenticate with sudo), e.g., your home directory, $ mkdir $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects If you have at least ~3G of free space, you could just copy the contents of the ./subjects dir from the freesurfer distribution into $HOME/subjects, $ cd $HOME$ pwd/Users/<username>$ ( cd  /Applications/freesurfer/7.1.1; tar cpf - subjects) | tar xpf - $ ls subjectsREADME*             cvs_avg35/          fsaverage3/         fsaverage6/         rh.EC_average/ V1_average/         cvs_avg35_inMNI152/ fsaverage4/         fsaverage_sym/      sample-001.mgz* bert/               fsaverage/          fsaverage5/         lh.EC_average/      sample-002.mgz* You can always start again from scratch after processing files by removing ./subejcts under your $HOME directory and copy the files over again via the tar command (w/o touching the installed freesurfer distribution). - R. On Apr 18, 2021, at 04:41, バキット・ムダシル <m-bakhit(a)fmu.ac.jp> wrote:        External Email - Use Caution        Thanks Douglas. Here what happened. I did as you said and moved the $SUBJECTS_DIR out of the /Applications folder to somewhere in my home folder. Still the same error. But when I did ran the command through freesurfer 6 it worked fine even in the /Applications folder. Also, a freesurfer 7 in an Ubuntu virtual machine worked fine. So I think it has to do with something in the freesurfer 7.1.1 version I have in my computer.I would like to add a question if you don’t mind. Since I found here in the forum that the average is in the MNI305 space, how I can make an average of my sample in MNI152 space from the start?ThanksMudathirOn Apr 14, 2021, at 23:26, Douglas N. Greve <dgreve(a)MGH.HARVARD.EDU> wrote:It looks like you do there, but downstream you might not. In general, macs don't like to give you permission in the apps folder. Try pointer your SUBJECTS_DIR to another location, eg, in your home directoryOn 4/6/2021 8:44 PM, バキット・ムダシル wrote:        External Email - Use Caution        I Think I have a permission. I ran chmod -R u+rwX to make sure, but the error was the same. Can you confirm from below please?\mudathirbakhit$ ls -l $FREESURFER_HOME/total 568drwxr-xr-x   39 mudathirbakhit  admin   1248 Mar 18 20:24 6..0.0-rwxr-xr-x    1 mudathirbakhit  wheel   3240 Aug 12  2020 ASegStatsLUT.txt-rwxr-xr-x    1 mudathirbakhit  wheel  47514 Aug 12  2020 DefectLUT.txt-rwxr-xr-x@   1 mudathirbakhit  wheel  89181 Aug 12  2020 FreeSurferColorLUT.txt-rwxr-xr-x    1 mudathirbakhit  wheel  18152 Aug 12  2020 FreeSurferEnv.csh-rwxr-xr-x    1 mudathirbakhit  wheel  18223 Aug 12  2020 FreeSurferEnv.shdrwxrwxr-x@   3 mudathirbakhit  wheel     96 Mar 16 13:11 Freeview.appdrwxr-xr-x    3 mudathirbakhit  wheel     96 Mar 17 10:06 Freeview_backup.app-rwxr-xr-x@   1 mudathirbakhit  wheel  28381 Aug 12  2020 SegmentNoLUT.txt-rwxr-xr-x    1 mudathirbakhit  wheel   1358 Aug 12  2020 SetUpFreeSurfer.csh-rwxr-xr-x    1 mudathirbakhit  wheel   1350 Aug 12  2020 SetUpFreeSurfer.sh-rwxr-xr-x@   1 mudathirbakhit  wheel   4104 Aug 12  2020 Simple_surface_labels2009.txt-rwxr-xr-x    1 mudathirbakhit  wheel  25476 Aug 12  2020 WMParcStatsLUT.txt-rw-r--r--@   1 mudathirbakhit  staff   2718 Apr  1 14:13 aparc+aseg.txtdrwxr-xr-x  126 mudathirbakhit  wheel   4032 Apr  7 07:22 averagedrwxr-xr-x  766 mudathirbakhit  wheel  24512 Mar 17 10:06 bin-rwxr-xr-x    1 mudathirbakhit  wheel     47 Aug 12  2020 build-stamp.txtdrwxr-xr-x    3 mudathirbakhit  wheel     96 Mar 17 19:35 colordrwxr-xr-x    3 mudathirbakhit  wheel     96 Aug 12  2020 diffusiondrwxr-xr-x   37 mudathirbakhit  wheel   1184 Aug 12  2020 docsdrwxr-xr-x    3 mudathirbakhit  wheel     96 Aug 12  2020 etcdrwxr-xr-x    5 mudathirbakhit  wheel    160 Aug 12  2020 fsafddrwxr-xr-x    6 mudathirbakhit  wheel    192 Apr  7 07:22 fsfastdrwxr-xr-x    6 mudathirbakhit  wheel    192 Apr  7 07:22 lib-rw-r--r--@   1 mudathirbakhit  wheel     55 Feb 17 09:40 license.txtdrwxr-xr-x  185 mudathirbakhit  wheel   5920 Apr  7 07:22 matlabdrwxr-xr-x   11 mudathirbakhit  wheel    352 Apr  7 07:22 mni-rw-r--r--@   1 mudathirbakhit  staff    641 Apr  6 16:13 par.txtdrwxr-xr-x    8 mudathirbakhit  wheel    256 Apr  7 07:22 pythondrwxr-xr-x    3 mudathirbakhit  wheel     96 Aug 12  2020 sessions-rwxr-xr-x    1 mudathirbakhit  wheel    134 Aug 12  2020 sources.csh-rwxr-xr-x    1 mudathirbakhit  wheel    132 Aug 12  2020 sources.shdrwxr-xr-x+  42 mudathirbakhit  wheel   1344 Apr  7 09:37 subjects-rwxr-xr-x    1 mudathirbakhit  wheel   1681 Aug 12  2020 tkmeditParcColorsCMAdrwxr-xr-x   38 mudathirbakhit  wheel   1216 Apr  7 07:22 trctrain-rwxr-xr-x    1 mudathirbakhit  wheel    972 Aug 12  2020 uninstall.shOn Apr 6, 2021, at 22:30, Douglas N. Greve <dgreve(a)MGH.HARVARD.EDU> wrote:Do you have write permissions to/Applications/freesurfer/subjectsOf not on a macOn 4/6/2021 6:39 AM, バキット・ムダシル wrote:        External Email - Use CautionHi,I am trying to make an average subject but when the process reaches mris_average_surface it fails as seen below.My command was as follow:make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10Can you please guide me to solve this issue.ThanksMudathir############################################@# Making average lh.white surface ---------------------Tue Apr  6 19:23:39 JST 2021/Applications/freesurfer/subjects/avgsubjectmris_make_average_surface -i 7 -o white -sdir-out /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10reading vertex positions from white...---------------------------------------------------hemi            = lhavg_surf_name   = whitecanon_surf_name = sphere.regout_sname       = avgsubjectxform           = talairach.xfm---------------------------------------------------Is a directoryIs a directoryERROR: creating directory /ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surfmris_average_surface failedERROR: make_average_surface#################################################_______________________________________________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/188o71fPj5Qr_j5Mfrzogt2krsKPOefJ8asGD0… 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/1hlFCV0MUrh_jtrWBZlJB7SU1uXzpdoDFwAz7j… Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/188o71fPj5Qr_j5Mfrzogt2krsKPOefJ8asGD0y8lpHnLI… 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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mris_average_surface fails
by バキット・ムダシル 18 Apr '21

18 Apr '21

External Email - Use Caution Hi, I am trying to make an average subject but when the process reaches mris_average_surface it fails as seen below. My command was as follow: make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 Can you please guide me to solve this issue. Thanks Mudathir ########################################### #@# Making average lh.white surface --------------------- Tue Apr 6 19:23:39 JST 2021 /Applications/freesurfer/subjects/avgsubject mris_make_average_surface -i 7 -o white -sdir-out /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 reading vertex positions from white... --------------------------------------------------- hemi = lh avg_surf_name = white canon_surf_name = sphere.reg out_sname = avgsubject xform = talairach.xfm --------------------------------------------------- Is a directory Is a directory ERROR: creating directory / ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf mris_average_surface failed ERROR: make_average_surface #################################################

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Running qcache on recon-all output
by Vishnu S 17 Apr '21

17 Apr '21

External Email - Use Caution Hello, I downloaded some FreeSurfer recon-all analyses from the ADNI dataset, but these analyses have been run without the qcache flag. Is there any way for me to re-analyse this with only the qcache flag? If so, how would I do this and how long would it take? Thanks for your help, Vishnu

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Task-based connectivity
by Kazuhisa Shibata 17 Apr '21

17 Apr '21

External Email - Use Caution Hi the list, I’d like to perform task-based connectivity such as generalized PPI based on results obtained by GLM at freesurfer. However, at least freesurfer 5.1.0 does not support such function. Only resting-state connectivity analysis was allowed in freesurfer. https://secure-web.cisco.com/1sexOeLhNkPN8Z3bn5abjthrTbMXIQ_FDPXvySkfm3Kli0… <https://secure-web.cisco.com/1sexOeLhNkPN8Z3bn5abjthrTbMXIQ_FDPXvySkfm3Kli0…> Since then, has such function been implemented in freesurfer and fsfast? If so, is there any webpage that describes how to perform it? If not, it seems necessary for me to transfer freesurfer surface data to CONN or other software like Generalized PPI toolbox. Does anyone have experience for this? If so, do you know any helpful documentation for it? https://secure-web.cisco.com/1kd5f_e9wnp_Q-jk6Fa1Nex_rQiyaV5YLCxYpT61rgTqPE… <https://secure-web.cisco.com/1kd5f_e9wnp_Q-jk6Fa1Nex_rQiyaV5YLCxYpT61rgTqPE…> https://secure-web.cisco.com/1d8170Se4bSakirggALI9YRg8jtSsFsA_EziRfhR5tvTNj… <https://secure-web.cisco.com/1d8170Se4bSakirggALI9YRg8jtSsFsA_EziRfhR5tvTNj…> Thank you very much for your help in advance! Best, Kaz -- Kazuhisa Shibata Team Leader Lab for Human Cognition and Learning Center for Brain Science RIKEN https://secure-web.cisco.com/1ROGmGYauHN9kDMMqdx7YcnyWqL-60MNWgMfD1P5crCo78… kazuhisa.shibata(a)riken.jp kazuhisa.shibata(a)gmail.com

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Curvature Stats func. error among step by step in recon-all process
by Yoonho Hwang 16 Apr '21

16 Apr '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute cortical thickness and to analyze it between groups. So I perform "recon-all", but rather than using recon-all -all, some problems arise while performing each of the steps in it. These problems are as follwing. *1. By perform "Curvature Stats" of recon-all in parallel, This process is required for ?h.curv file. This file is created after -white or -whitesurf process, but looking at recon-all file in /usr/local/freesurfer/bin/, -whitesurf is running after this process, so I think so, Is it correct to move position of curvature stats after the pialsurf to fix the error?* *2. Looking at https://secure-web.cisco.com/1GkMeZvnVnQ05ojl-46PZk8Ur4cuLzS11EOrMEhAlenwlb… <https://secure-web.cisco.com/1GkMeZvnVnQ05ojl-46PZk8Ur4cuLzS11EOrMEhAlenwlb…> and recon-all file, because order of autorecon -all is different between two reference, I am confused. Can you please tell me which one to refer to?* 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu release 18.04.1 3) uname -a: Linux LABPC 5.4.0-70-generic #78~18.04.1-Ubuntu SMP Sat Mar 20 14:10:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you very much. Sincerely, Yoonho -- *Hwang, Yoonho* *Medical Image Processing Laboratory (MIPL),* *Department of Biomedical Engineering, Yonsei University.* *#218 Sanhak-Kwan, 1, Yeonsedae-gil, Heungeop-myeon, Wonju,* *Gangwon-do, 26493, Republic of Korea.* *Office: +82-33-760-2499* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

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CVS register
by Jones, Richard 16 Apr '21

16 Apr '21

External Email - Use Caution I have a couple of questions regarding CVS register. I'm using Freesurfer 7.1 and I want to align some QSM images in order to analyze some sub-cortical structures that are not defined by Freesurfer (red nucleus, substantia nigra). I ran CVS register to register a subject to MNI152 space and the "final_CVSmorph_tocvs_avg35_inMNI152_norm.mgz file was in excellent registration with the mni152 brain, but when I looked at the corresponding aseg file (final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz) the general registration was good but it appears to be slightly smaller than the MNI152 brain (see image below), is that to be expected? [cid:image002.png@01D72BAA.D8C3E330][cid:image004.png@01D72BAA.D8C3E330] To move the QSM image into MNI space I can use one of the echoes used as the input for the QSM processing to derive the registration between the QSM image and the T1 volume using BBR register to give me a transformation file "qsm2anat.dat". Looking at the documentation it seems I have to use CreateMorph to recreate the morph required to shift the QSM data from freesurfer to MNI space (and I'm a little confused about exactly what the morph final_CVSmorph_tocvs_avg35_inMNI152.m3z actually does). For CreateMorph I'm a little uncertain which of the files shown above I should use for the -in option to CreateMorph and for the -template option do I just specify the brain.mgz from /subjects/cvs_avg35_inMNI152/mri directory? Having created the morph file "my _morph_file.m3z" I could use apply_morph having first transformed the QSM image into freesurfer space, but would it be easier to use mri_vol2vol with the following options:- mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz --m3z $SUBJECTS_DIR/my_subject/cvs/my _morph_file.m3z --noDefM3zPath \ -reg qsm2anat.dat --mov my_qsm_image.nii -out my_qsm_image_in_mni152.nii --interp trilin --no-save-reg Thanks, Richard

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Freesurfer April 2021