Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

longitudinal trac -prep missing outputs
by Zeng, Qi 20 May '20

20 May '20

External Email - Use Caution Hi, I was running longitudinal trac-all. After the 3rd step -path was finished, I found that multiple pathways were missing (e.g. fminor). I traced back, realizing outputs from its first step trac-prep were missing corresponding pathways in SUBJ_base/dlabel/mni/fminor. However, the scripts of SUBJ_base_long_ses-1 and ses-2 both claimed "trac-preproc finished without error". I double checked the bval, bvec and DTI and increased the memory limit, the same problem still exists. So I was wondering how to fix it. Attached the log file of SUBJ_base of trac -prep. Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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Infant Freesurfer: infant_recon_all error
by Fleur Warton 20 May '20

20 May '20

External Email - Use Caution Hi, I recently installed the Infant FreeSurfer package. When I try to run infant_recon_all (specific command: infant_recon_all --s SUBJ --age AGE) I get the error if: Expression Syntax I tried switching shells from bash to tcsh but got the same error. The FreeSurfer version is freesurfer-infant-20200205 My platform is Ubuntu 18.04 Any suggestions how to fix this? Kind regards, Fleur

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Freeview on debian
by Gian Marco Duma 20 May '20

20 May '20

External Email - Use Caution Hi everyone, I have a problem with freeview. My university created for me a virtual machine in a small analysis cluster. Unfortunately, they installed Debian 4.19.98. I read that freeview has some problems with Debian, and in fact I am not able to open it. Unfortunately I need to visualize the data because we are conducting an anatomical study with patients with lesions. All the processes I ran until now, like automatic segmentation and surface generation like recon all, worked perfectly, but I need to visualize the data. Do you have suggestions to solve this problem? Thanks

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Freesurfer version 7.0.0 and hippocampal segmentation
by Vanessa Cropley 20 May '20

20 May '20

External Email - Use Caution Hello Freesurfer team, I have just become aware of the release notes concerning v7.0.0 being recalled and not to be used, with the recommendation to use v7.1.0 instead: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes I have a couple of questions about the implications of this recall. We have processed a large dataset using freesurfer version 6, with all subjects being processed (recon-all) with the same version/platform. We would now like to segment the hippocampal subfields using the enhanced version of the module as outlined here: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields which requires Freesurfer 7. We have successfully run the hippocampal segmentation using freesurfer_v7.0.0_dev_20200405 (7.1 was not available at the time). My questions: 1. Given the recall of v7.0.0, does this mean that we should re-do the hippocampal segmentation that used v7.0.0 with v7.1.0? In other words, are all functions within v7.0.0 to be avoided, or just the recon-all stream? 2. Given that the recon-all was processed with v6, is it ok to perform the hippocampal subfield segmentation with v7? I understand that it is fine to perform post-processing functions outside the recon-all stream with newer versions (provided recon-all was done with the same version). Is my understanding correct? Thank you for your assistance. - Vanessa

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Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask
by Elena Pozzi 19 May '20

19 May '20

External Email - Use Caution Thanks so much!

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Re: [Freesurfer] Freesurfer Digest, Vol 195, Issue 47
by Hua, Jessica 19 May '20

19 May '20

External Email - Use Caution After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters. The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the adjusted values accounting for age, sex, and ICV (this is a three group design). The X matrix was 240x12 (see attached file) * Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3 * Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3 * Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3 * Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3 * Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3 * Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3 * Column 10: zICV for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 11: 0s for Group 1 and zICV for Group 2 and 0s for Group 3 * Column 12: 0s for Group 1 and 0s for Group 2 and zICV for Group 3 I was not sure how to modify the last line in your code in order to calculate adjusted values accounting for age, sex, and ICV for each participant. Your code: There is not an easy way to do it, but you can do it in matlab cd glmdir X = load('Xg.dat'); y = load('perm.th30.abs.y.ocn.dat'); beta = inv(X'*X)*X'*y; yhat = X(:,[i j k ...]*beta([i j k ...]) where i j k ... indicate the factors you want keep in your data. Each factor gets a column in the design matrix (and a beta). If you need help figuring this out, send the fsgd file. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri ________________________________ 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 <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Tuesday, May 19, 2020 10:18 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 195, Issue 47 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. Re: vol2subfield single time course from multiple regions (stdp82(a)virgilio.it) 2. Re: Longitudinal edits on norm.mgz instead of brainmask (Douglas N. Greve) 3. Re: Volume timeseries to native and fsaverage (Douglas N. Greve) 4. Re: Group Analysis Covariates (Hua, Jessica) 5. Re: Group Analysis Covariates (Hua, Jessica) 6. Re: qdec and mris_anatomical_stats help (Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience) 7. Re: Robust Regression with Univariate LME (Hua, Jessica) 8. Re: Longitudinal edits on norm.mgz instead of brainmask (Elena Pozzi) 9. Freesurfer hippocampal segmentation in patient with temporal lesion (Linda Zhang) 10. Unable to visualize last Topics (Ferraro, Pilar) 11. freesurfer subcortical segmentation (ZhangBo) 12. FREESURFER-7.1: recon-all exited with error "ERROR: cannot find or read transforms/talairach.m3z" (Safi Ullah .) ---------------------------------------------------------------------- Message: 1 Date: Mon, 18 May 2020 18:46:35 +0200 (CEST) From: stdp82(a)virgilio.it Subject: Re: [Freesurfer] vol2subfield single time course from multiple regions To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Cc: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Message-ID: <163566753.837213.1589820395908(a)mail1.virgilio.it> Content-Type: text/plain; charset="utf-8" External Email - Use Caution thanks! > Il 18 maggio 2020 alle 16.23 Bruce Fischl < fischl(a)nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > ha scritto: > > > --replaceonly <label 1 to remove> <label 1 to replace with> \ > --replaceonly <label 2 to remove> <label 2 to replace with> \ > . > . > . > > On Mon, 18 May 2020, stdp82(a)virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > External Email - Use Caution > > > > As reported in previous mails I have do it but with some problems. > > > > Moreover, how can I do with multiple arguments (more than 2)? > > > > > > > > Il 17 maggio 2020 alle 21.30 Bruce Fischl < > > fischl(a)nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > ha scritto: > > > > > > Hi Stefano > > > > --replaceonly takes two arguments - the label you want to replace and > > the > > one you want to replace it with > > > > cheers > > Bruce > > > > > > On Sun, 17 May 2020, stdp82(a)virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > External Email - Use Caution > > > > just a kind reminder > > > > many thanks > > > > > > > > Il 15 maggio 2020 alle 1.05 stdp82(a)virgilio.it mailto:stdp82@virgilio.it ha scritto: > > > > > > > > mri_binarize --i > > $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz > > --replaceonly 8204 --replaceonly 8205 --replaceonly 8206 > > --replaceonly 8217 --replaceonly 8218 --o > > $SUBJECTS_DIR/R-Intralaminar.mgz > > > > ERROR: Option 8205 unknown > > > > > > mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz > > --replaceonly 8204 --replaceonly 8205 --replaceonly 8217 > > --replaceonly > > 8218 --o $SUBJECTS_DIR/R-Intralaminar.mgz > > > > ERROR: Option 8217 unknown > > Il 14 maggio 2020 alle 17.39 "Douglas N. Greve" > > < dgreve(a)mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha scritto: > > > > > > > > Just add more --replaceonly args > > > > > > > > On 5/14/2020 10:38 AM, stdp82(a)virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Moreover, how can I merge, with mri_binarize, more > > thalamic regions? > > > > > > > > e.g. 8204 8205 8206 8217 8218 > > > > > > > > Il 13 maggio 2020 alle 23.03 "Douglas N. > > Greve" < dgreve(a)mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha > > scritto: > > > > > > > > It problably means that seg 8130 does > > not exist in the input mgz. Can you > > confirm that it does? > > > > > > > > On 5/13/2020 12:51 PM, > > stdp82(a)virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > External Email - Use > > Caution > > > > > > > > indeed. I would like to merge two > > regions and extract the fMRI time serie. > > if no difference is there, somewhat is > > wrong. the L-VP file contains the same > > information of ThalamicNuclei.v10.T1. > > > > > > > > thanks > > > > > > > > Il 13 maggio 2020 alle 17.02 > > "Douglas N. Greve" > > < dgreve(a)mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha > > scritto: > > > > > > > > That means there is no > > difference > > > > > > > > On 5/13/2020 10:47 AM, > > stdp82(a)virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > External Email - Use > > Caution > > > > > > > > is the command line ok? > > > > > > > > by running > > > > > > > > mri_binarize --i > > ThalamicNuclei.v10.T1.mgz > > --replace-only 8130 8133 --o > > L-VP.mgz > > > > > > > > mri_diff --po > > mri/ThalamicNuclei.v10.T1.mgz > > L-VP.mgz > > > > > > > > I obtain > > diffcount 0 > > > > > > > > Il 12 maggio 2020 alle > > 0.53 > > stdp82(a)virgilio.it mailto:stdp82@virgilio.it ha > > scritto: > > > > > > > > by running > > mri_diff --po > > mri/ThalamicNuclei.v10.T1.mgz > > L-VP.mgz > > I obtain > > diffcount 0 > > > > > > > > Il 11 maggio > > 2020 alle 19.18 > > "Douglas N. > > Greve" > > < dgreve(a)mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > > > ha scritto: > > > > > > > > Try running this > > to see if there > > is a difference > > mri_diff --po > > ThalamicNuclei.v10.T1.mgz > > Left-Ventroposterior.mgz > > Sometimes it is > > not easy to see > > a difference > > that is just a > > few voxels > > > > > > > > On 5/11/2020 > > 3:02 AM, > > stdp82(a)virgilio.it mailto:stdp82@virgilio.it > > wrote: > > > > > > > > External > > Email - > > Use > > Caution > > > > > > > > By > > visualizing > > the output > > by > > freeview, > > I found > > that it > > was the > > same > > of ThalamicNuclei.v10.T1.mgz. > > > > > > > > Thanks > > > > > > > > Il > > 11 > > maggio > > 2020 > > alle > > 2.19 > > Bruce > > Fischl > > < > > fischl(a)nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > > > ha > > scritto: > > > > > > Hi Stefano > > > > can you > > elaborate? > > Why do you > > suspect > > there is > > an error? > > > > cheers > > Bruce > > On Mon, 11 > > May > > 2020, > > stdp82(a)virgilio.it mailto:stdp82@virgilio.it > > wrote: > > > > > > > > External > > Email > > - > > Use > > Caution > > > > Please, > > could > > you > > check > > the > > command > > line. > > I > > suspect > > that > > an > > error > > is > > there. > > Thanks. > > Stefano > > > > mri_binarize > > --i > > ThalamicNuclei.v10.T1.mgz > > --replace-only > > 8130 > > > > 8133 > > --o > > Left-Ventroposterior.mgz > > > > > > > > Il > > 30 > > aprile > > 2020 > > alle > > 18.51 > > "Douglas > > N. > > Greve" > > < > > dgreve(a)mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > > > ha > > scritto: > > > > > > > > You > > can > > use > > mri_binarize > > --i > > ThalamicNuclei.v10.T1.mgz > > --replace-only > > segid > > segidreplace > > ... > > --o > > newseg.mgz > > to > > create > > a > > new > > segmentation > > with > > merged > > segments, > > then > > using > > vol2subfield > > with > > the > > newseg > > seg > > as > > --sf > > > > > > > > On > > 4/29/2020 > > 7:57 > > PM, > > stdp82(a)virgilio.it mailto:stdp82@virgilio.it > > wrote: > > > > > > > > External > > Email > > - > > Use > > Caution > > > > > > > > Hi > > list, > > > > > > > > vol2subfield > > --i > > fmcpr.nii.gz > > --reg > > register.dof6.lta > > --sf > > ThalamicNuclei.v10.T1.mgz > > --stats > > stats.dat > > --avgwf > > avgwf.dat > > --avgwfvol > > avgwfvol.mgz > > --o > > f2subf.nii.gz > > > > > > > > extracts > > the > > time > > course > > from > > each > > thalamic > > subregions. > > > > > > > > If > > I > > would > > like > > to > > merge > > multiple > > regions > > (e.g. --id > > 8115 > > --id > > 8116) > > and > > extract > > a > > single > > time > > course > > from > > them, > > which > > is > > the > > way? > > > > > > > > Thanks > > > > > > > > Stefano > > > > > > > > _______________________________________________ > > Freesurfer > > mailing > > list > > Freesurfer(a)nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer > > mailing > > list > > Freesurfer(a)nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > Freesurfer > > mailing > > list > > Freesurfer(a)nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > The 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 Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline > > . 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. > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Re: [Freesurfer] Freeview on debian
by fsbuild 19 May '20

19 May '20

External Email - Use Caution Hello Gian, Maybe you can report back with the version of Debian linux you are using so we could look into it. You could try downloading and running the Ubuntu VM image we have with freesurfer 6 and 7 beta release installed on it.  If you are going to run the VM on a linux machine, then you should still be able to follow the instructions listed for setting up the VM on either the Mac or Windows after you install VirtualBox on your linux machine.  The links to the VirtualBox setup instructions for MacOS and Windows are here,https://surfer.nmr.mgh.harvard..edu/fswiki/VM_67 The link to the Ubuntu VM image is on this page where it lists FStutorial_clone_2.7z followed by the link when you click on “image”.  You will need a 7zip program to uncompress it (as explained in Mac and Windows instructions). Once you get the Ubuntu VM running and login as userid developer, you can update the beta 7 release to the latest 7.1.0 release with the instructions below. You can email me directly if you run into something. - R. - - - - -  Updating Ubuntu FS 7 beta release to the current 7.1.0 release - - - - Log into the Ubuntu VM as aid developer. Download the latest release - currently 7.1.0 - from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-lin… Let's assume after the download the archive file is located in your downloads folder under the path, ~/Downloads/freesurfer-linux-centos7_x86_64-7.1.0.tar.gz Locate your previous version 7 release under the path /usr/local/freesurfer $ ls /usr/local/freesurfer 6.0.0-1  7.0.0-1 Remove the previous version 7 release, here 7.0.0-1, $ cd /usr/local/freesurfer $ sudo rm -rf  7.0.0-1 Expand the archive for the new release from your downloads folder, $ sudo  tar  zxpf  ~/Downloads/freesurfer-linux-centos7_x86_64-7.1.0.tar.gz Now move the newly created ./freesurfer subdirectory from the archive to be the name of the new release, $ sudo mv freesurfer 7.1.0-1 Check to see files are there, $ ls 7.1.0-1 <output deleted> Finally, replace your existing $HOME/.bashrc file with the attached bashrc file which will allow you to run either the 6.0.0 or 7.1.0 release.  NOTE - if you have made changes to your $HOME/..bashrc file since you started using the VM, then you may want to merge your current $HOME/.bashrc with the contents of the attached bashrc in order not to lose your changes. You could also diff the 2 files and add manually edit in the changes from the attached bashrc. With the new bashrc in your downloads folder as ~/Downloads/bashrc, then to diff the files, $ diff  ~/Downloads/bashrc  $HOME/.bashrc To simply replace the old bashrc in its entirety, $ cp -p -f  ~/Downloads/bashrc  $HOME/.bashrc Once your new $HOME/.bashrc file is in place (which should use use the 7.1.0-1 release by default), then start a new terminal window.  You should see the following output: -------- freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /usr/local/freesurfer/7.1.0-1 FSFAST_HOME       /usr/local/freesurfer/7.1.0-1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /usr/local/freesurfer/7.1.0-1/subjects TUTORIAL_DATA     /home/developer/tutorial_data MNI_DIR           /usr/local/freesurfer/7.1.0-1/mni WARNING: /usr/local/freesurfer/7.1.0-1/fsl_507/bin does not exist. FSL_DIR           /usr/local/freesurfer/7.1.0-1/fsl_507 On May 19, 2020, at 12:14, Gian Marco Duma <gianmarco.duma(a)phd.unipd.it> wrote:        External Email - Use Caution        Hi everyone, I have a problem with freeview. My university created for me a virtual machine in a small analysis cluster. Unfortunately, they installed Debian 4.19.98. I read that freeview has some problems with Debian, and in fact I am not able to open it. Unfortunately I need to visualize the data because we are conducting an anatomical study with patients with lesions. All the processes I ran until now, like automatic segmentation and surface generation like recon all, worked perfectly, but I need to visualize the data. Do you have suggestions to solve this problem?Thanks_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Uploading fs7.1 to hms o2 cluster
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 19 May '20

19 May '20

?Hi, Can someone from the martinos center who has access to /n/app/martinos/freesurfer in the Harvard O2 cluster upload freesurfer 7.1? Right now it just has freesufer 6.0. Thanks in advance, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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freesurfer subcortical segmentation
by ZhangBo 19 May '20

19 May '20

External Email - Use Caution Hi teams, Does freesurfer supports calculate subcortical volumes like globus pallidus internus, globus pallidus externa, subthalamic nucleus , ventral intermedius nucleus, like these areas? Thanks

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Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask
by Elena Pozzi 19 May '20

19 May '20

External Email - Use Caution Hi Douglas, Thank you very much for your answer. I tried the command you suggested and it did not seem to transfer the edits, so I added the flag -keep_mask_deletion_edits and that seems to work. Would you mind confirming that the final command mri_mask -keep_mask_deletion_edits brainmask.mgz norm.mgz brainmask.mgz is safe to run to transfer the edits (i.e., voxel deleted) from the norm.mgz to the brainmask.mgz? Thanks again! Elena

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