Re: [Freesurfer] Contents of Freesurfer digest Vol 200, Issue 28 error trac all prep (Yendiki, Anastasia)
External Email - Use Caution
Hi Anastasia,
Thank you so much for your reply. I omitted a very important information. I am working with left hemisphere stroke data. On a visual check I see that recon all worked well on all the participants (big and small lesions). Although trac all worked for some participants with a smaller lesion, I suspect this failure may be due to the presence of a bigger lesion. In order to test if this is the case, I could perform trac all only on the right hemisphere. Can you tell me how to perform tracall only on the right hemisphere? I tried to edit the config file but it did not work. Please, let me know if you have other suggestions on what can go wrong as well.
Thank you in advance Best regards Ileana
Ileana Camerino
PhD candidate Donders Institute for Brain, Cognition and Behaviour
Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618
On 14/10/2020, 18:01, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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You can reach the person managing the list at freesurfer-owner@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: error trac all prep (Yendiki, Anastasia) 2. Postdoc and PhD positions @ BrainLENS Lab w/ Fumiko Hoeft {Disarmed} (Jieyin Feng) 3. Help with creating contrast matrix - 6 classes and 3 variables (Paul Dhami) 4. Reliability and sensitivity of two whole-brain segmentation approaches ? ASEG and SAMSEG (Donatas Sederevicius) 5. tk applications failing to launch on VM (Windows) (Mcnorgan, Christopher)
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Message: 1 Date: Tue, 13 Oct 2020 20:20:03 +0000 From: "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu Subject: Re: [Freesurfer] error trac all prep To: "Freesurfer@nmr.mgh.harvard.edu" Freesurfer@nmr.mgh.harvard.edu Message-ID: MN2PR04MB57575E2B4044A5177DC947F08A040@MN2PR04MB5757.namprd04.prod.outlook.com Content-Type: text/plain; charset="us-ascii"
Hi Ileana - It looks like it fails on the left uncinate. Is there any artifact or missing part of the brain or brain mask, either in the diffusion scan or the T1 scan, in a location that would affect the uncinate?
Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Camerino, I.L. (Ileana) i.camerino@psych.ru.nl Sent: Tuesday, October 13, 2020 11:12 AM To: Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] error trac all prep
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to run the tractography analyses as described on the Tracula tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), I tried the all pipeline for one subject and it worked. I tried to run in parallel for the rest of the subjects and for three of them I get the following error when I run the trac all -prep command:
#!/bin/bash export FREESURFER_HOME=/opt/freesurfer/6.0; source $FREESURFER_HOME/SetUpFreeSurfer.sh; export SUBJECT_DIR=$/project/3015068.01/ilecam/Reolang/Freesurfer for i in `cat /project/3015068.01/ilecam/Reolang/scripts/list_trac_all_prep2.txt`; do trac-all -prep -c /project/3015068.01/ilecam/Reolang/Freesurfer/${i}/Tracula_out/tracula_config.txt; done
here below the content of trac-all.eror ------------------------------ SUBJECT sub-056 DATE Fri Oct 9 16:18:01 CEST 2020 USER ilecam HOST dccn-c029.dccn.nl PROCESSOR x86_64 OS Linux Linux dccn-c029.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.54.2.2 2016/12/27 16:47:14 zkaufman Exp $ /opt/freesurfer/6.0/bin/trac-preproc PWD /project/3015068.01/ilecam/Reolang/scripts CMD /opt/freesurfer/6.0/bin/dmri_train --outdir /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.sub-056.18934.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.b! br.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dl! abel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.b! br.nii.g z dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni/aparc+aseg_mask.nii.gz --fa /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dmri/dtifit_FA.nii.gz --cptdir /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/diff --reg /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dmri/xfms/mni2diff.bbr.mat --ncp! ts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc
I've searched the list and no similar errors have been reported. Please can anyone share their thoughts on how to trouble-shoot this one?
Also, Ive attached the recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer/6.0 build-stamp.txt: Platform: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c2) 3) uname -a: Linux dccn-c046.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux) recon-all.log: see attached
thank you in advance
Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618
Hi Ileana - You can set the "pathlist" to include a specific set of pathways. In the example config file the pathlist includes all 18 pathways, but you can change it, e.g., to only include the rh ones: https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
That said, TRACULA doesn't use the conventional type of streamline tractography that would "stop" in the middle of a tract (e.g., due to a lesion), so I'd be interested in what you find. If you continue to have issues after running these tests, you can upload an example subject for me to look at here: https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks, Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Camerino, I.L. (Ileana) i.camerino@psych.ru.nl Sent: Monday, October 26, 2020 7:08 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Contents of Freesurfer digest Vol 200, Issue 28 error trac all prep (Yendiki, Anastasia)
External Email - Use Caution
Hi Anastasia,
Thank you so much for your reply. I omitted a very important information. I am working with left hemisphere stroke data. On a visual check I see that recon all worked well on all the participants (big and small lesions). Although trac all worked for some participants with a smaller lesion, I suspect this failure may be due to the presence of a bigger lesion. In order to test if this is the case, I could perform trac all only on the right hemisphere. Can you tell me how to perform tracall only on the right hemisphere? I tried to edit the config file but it did not work. Please, let me know if you have other suggestions on what can go wrong as well.
Thank you in advance Best regards Ileana
Ileana Camerino
PhD candidate Donders Institute for Brain, Cognition and Behaviour
Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618
On 14/10/2020, 18:01, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to freesurfer@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@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@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: error trac all prep (Yendiki, Anastasia) 2. Postdoc and PhD positions @ BrainLENS Lab w/ Fumiko Hoeft {Disarmed} (Jieyin Feng) 3. Help with creating contrast matrix - 6 classes and 3 variables (Paul Dhami) 4. Reliability and sensitivity of two whole-brain segmentation approaches ? ASEG and SAMSEG (Donatas Sederevicius) 5. tk applications failing to launch on VM (Windows) (Mcnorgan, Christopher)
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Message: 1 Date: Tue, 13 Oct 2020 20:20:03 +0000 From: "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu Subject: Re: [Freesurfer] error trac all prep To: "Freesurfer@nmr.mgh.harvard.edu" Freesurfer@nmr.mgh.harvard.edu Message-ID: MN2PR04MB57575E2B4044A5177DC947F08A040@MN2PR04MB5757.namprd04.prod.outlook.com
Content-Type: text/plain; charset="us-ascii"
Hi Ileana - It looks like it fails on the left uncinate. Is there any artifact or missing part of the brain or brain mask, either in the diffusion scan or the T1 scan, in a location that would affect the uncinate?
Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Camerino, I.L. (Ileana) i.camerino@psych.ru.nl Sent: Tuesday, October 13, 2020 11:12 AM To: Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] error trac all prep
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to run the tractography analyses as described on the Tracula tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), I tried the all pipeline for one subject and it worked. I tried to run in parallel for the rest of the subjects and for three of them I get the following error when I run the trac all -prep command:
#!/bin/bash export FREESURFER_HOME=/opt/freesurfer/6.0; source $FREESURFER_HOME/SetUpFreeSurfer.sh; export SUBJECT_DIR=$/project/3015068.01/ilecam/Reolang/Freesurfer for i in `cat /project/3015068.01/ilecam/Reolang/scripts/list_trac_all_prep2.txt`; do trac-all -prep -c /project/3015068.01/ilecam/Reolang/Freesurfer/${i}/Tracula_out/tracula_config.txt; done
here below the content of trac-all.eror ------------------------------ SUBJECT sub-056 DATE Fri Oct 9 16:18:01 CEST 2020 USER ilecam HOST dccn-c029.dccn.nl PROCESSOR x86_64 OS Linux Linux dccn-c029.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.54.2.2 2016/12/27 16:47:14 zkaufman Exp $ /opt/freesurfer/6.0/bin/trac-preproc PWD /project/3015068.01/ilecam/Reolang/scripts CMD /opt/freesurfer/6.0/bin/dmri_train --outdir /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.sub-056.18934.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.b! br.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dl! abel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.b! br.nii.g z dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni/aparc+aseg_mask.nii.gz --fa /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dmri/dtifit_FA.nii.gz --cptdir /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/diff --reg /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dmri/xfms/mni2diff.bbr.mat --ncp! ts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc
I've searched the list and no similar errors have been reported. Please can anyone share their thoughts on how to trouble-shoot this one?
Also, Ive attached the recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer/6.0 build-stamp.txt: Platform: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c2) 3) uname -a: Linux dccn-c046.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux) recon-all.log: see attached
thank you in advance
Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618
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Message: 2 Date: Tue, 13 Oct 2020 16:26:46 -0400 From: Jieyin Feng jieyinfeng0505@gmail.com Subject: [Freesurfer] Postdoc and PhD positions @ BrainLENS Lab w/ Fumiko Hoeft {Disarmed} To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Message-ID: CAAz+7TExQ=gBDDCy=S_i-TuRAOJiZymp3ABmuL_TDLR5EAjWVQ@mail.gmail.com Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi All,
*We have openings for Postdoc and PhD positions @ UConn brainLENS Lab: **https://www.brainlens.org/employment https://www.brainlens.org/employment*
*Fumiko Hoeft MD PhD*, Professor of the Departments of Psychological Sciences, Mathematics, Neuroscience and Psychiatry ( https://psych.uconn.edu/person/fumiko-hoeft/ https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fpsych.uconn.edu-252Fperson-252Ffumiko-2Dhoeft-252F-26data-3D04-257C01-257Cfumiko.hoeft-2540uconn.edu-257C7fa6eee5c92b4cca302f08d86f567d05-257C17f1a87e2a254eaab9df9d439034b080-257C0-257C0-257C637381764565086976-257CUnknown-257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0-253D-257C1000-26sdata-3DcOOMxd-252FOTRBHgFE9DO50WOYLe35Bg2P1iYaH1wVyw7g-253D-26reserved-3D0&d=DwMFAg&c=iORugZls2LlYyCAZRB3XLg&r=dtG_qwRsLq12hw7HJHokcrOXSYKdIqMu9b8edyK33Yk&m=LT1cfhpHjmJE3g8ZbJE2OXYbMwgk1UY8XfncCcB6Y14&s=kQt4f6RclVw-ZGSGdpNVcpkPRo3VXLdRFXi4gqYBO9k&e=), and Director of the Brain Imaging Research Center (https://birc.uconn.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fbirc.uconn.edu-252F-26data-3D04-257C01-257Cfumiko.hoeft-2540uconn.edu-257C7fa6eee5c92b4cca302f08d86f567d05-257C17f1a87e2a254eaab9df9d439034b080-257C0-257C0-257C637381764565096968-257CUnknown-257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0-253D-257C1000-26sdata-3DlcCgirkRnijQbOE7dRjtSHf05yM1PI3sv3NpAyoMHOQ-253D-26reserved-3D0&d=DwMFAg&c=iORugZls2LlYyCAZRB3XLg&r=dtG_qwRsLq12hw7HJHokcrOXSYKdIqMu9b8edyK33Yk&m=LT1cfhpHjmJE3g8ZbJE2OXYbMwgk1UY8XfncCcB6Y14&s=NZlMO9KuvCyZapwbXKBrEBzxD4fjz_GsfsLSuNdKJhc&e=) at the University of Connecticut in CT US, is now accepting applications of *up to two postdoctoral fellows* to begin sometime between now and the fall of 2021; and/or *two PhD students* to begin in the fall of 2021. Our bicoastal labs at UCSF and UConn (https://www.brainlens.org https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fwww.brainlens.org-252F-26data-3D04-257C01-257Cfumiko.hoeft-2540uconn.edu-257C7fa6eee5c92b4cca302f08d86f567d05-257C17f1a87e2a254eaab9df9d439034b080-257C0-257C0-257C637381764565096968-257CUnknown-257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0-253D-257C1000-26sdata-3DyBHeFWMw5UmxcXrCUOI-252BIv9e3YFEnrA6Btkd-252F2esqYg-253D-26reserved-3D0&d=DwMFAg&c=iORugZls2LlYyCAZRB3XLg&r=dtG_qwRsLq12hw7HJHokcrOXSYKdIqMu9b8edyK33Yk&m=LT1cfhpHjmJE3g8ZbJE2OXYbMwgk1UY8XfncCcB6Y14&s=U4X6MznK6nhd7QQKgpl1Hr8RC9WD1ZxyLc6yTWn2t-o&e=) have a strong track-record in interdisciplinary research spanning from theory, multimodal neuroimaging (fMRI, dMRI, TMS, MRS, EEG, etc), genetics, machine learning and network approaches, on topics relevant to reading development, dyslexia and resilience/compensatory mechanisms (see on the website). We are particularly interested in candidates who have a background or interest in behavioral genetics, and/or computational (machine learning / network) approaches that can be applied to neuroimaging data; and/or fetal/neonatal neuroimaging. The positions are fully funded, primarily by NIH grants, and by graduate research assistantships (GRAs). There are opportunities to be involved in federally funded and interdisciplinary graduate and postdoctoral training programs (NSF NRT https://slac.uconn.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fslac.uconn.edu-252F-26data-3D04-257C01-257Cfumiko.hoeft-2540uconn.edu-257C7fa6eee5c92b4cca302f08d86f567d05-257C17f1a87e2a254eaab9df9d439034b080-257C0-257C0-257C637381764565106960-257CUnknown-257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0-253D-257C1000-26sdata-3DluWqfbCLLcgo4xkp824CgahhY2MNKeEXnSX9LnBgtSg-253D-26reserved-3D0&d=DwMFAg&c=iORugZls2LlYyCAZRB3XLg&r=dtG_qwRsLq12hw7HJHokcrOXSYKdIqMu9b8edyK33Yk&m=LT1cfhpHjmJE3g8ZbJE2OXYbMwgk1UY8XfncCcB6Y14&s=MuXpaYVWjp6rXaYV7X8JGf5Zk20DVtgfUbvGbBVi4W4&e=, NIH T32 https://cncct.research.uconn.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fcncct.research.uconn.edu-252F-26data-3D04-257C01-257Cfumiko.hoeft-2540uconn.edu-257C7fa6eee5c92b4cca302f08d86f567d05-257C17f1a87e2a254eaab9df9d439034b080-257C0-257C0-257C637381764565106960-257CUnknown-257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0-253D-257C1000-26sdata-3DiWi6vMb0BTX35X1rofyVusWjDLZl3mNZW50rUwyFtI0-253D-26reserved-3D0&d=DwMFAg&c=iORugZls2LlYyCAZRB3XLg&r=dtG_qwRsLq12hw7HJHokcrOXSYKdIqMu9b8edyK33Yk&m=LT1cfhpHjmJE3g8ZbJE2OXYbMwgk1UY8XfncCcB6Y14&s=CQuH9RJJzGVLVu0S0dc04KtdqnBTaB9bvsry7VVqpnc&e=). Interested applicants should contact Prof. Fumiko Hoeft @ brainLENS@uconn.edu.
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Message: 3 Date: Tue, 13 Oct 2020 19:52:48 -0400 From: Paul Dhami pdhami06@gmail.com Subject: [Freesurfer] Help with creating contrast matrix - 6 classes and 3 variables To: freesurfer@nmr.mgh.harvard.edu Message-ID: CABqnCmBXcOa+1QDCVRdwcvMfkVwEwUzXZZEjmSWoihNFvDPC+w@mail.gmail.com Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear Freesurfer community,
I am having trouble with my contrast matrix, and would greatly appreciate any help with this.
I have 2 categorical variables, sex (2 levels) and training type (3 levels).
I also have three (continuous) variables: Age, percentage reduction in depression scores, and number of sessions.
I would like to assess the correlation between cortical thickness and % reduction in depression scores, while accounting for the effects of sex, training type, age, and number of sessions as nuisance variables.
Below is 1) my command line, 2) the FSGD fiile, and 3) the design matrix
1.
mri_glmfit.bin --y MDD-lh-thickness.mgh --fsgd Reduction_Correlation.fsgd.txt --C ME_ReductionCorrelation_Contrast.txt --fwhm 20 --surf fsaverage lh --glmdir /Users/prabhjotdhami/Desktop/CorticalThickness/Data/myGLM
2.
GroupDescriptorFile 1 Title MDD_correlation Class MaleMaxT Class MaleKahn Class MaleNone Class FemaleMaxT Class FemaleKahn Class FemaleNone Variables Age HRSD_Reduction SessionNumber Input yct-001 FemaleMaxT 24 62.5 20 Input yct-002 MaleKahn 18 70 20 Input yct-004 MaleMaxT 21 50 20 Input yct-005 MaleMaxT 24 25 20 Input yct-006 FemaleKahn 24 65.2173913 20 Input yct-012 FemaleKahn 17 71.42857143 20 Input yct-013 MaleMaxT 22 53.84615385 20 Input yct-014 FemaleMaxT 19 63.63636364 20 Input yct-015 FemaleMaxT 16 80.95238095 20 Input yct-016 FemaleKahn 24 65.2173913 20 Input yct-017 FemaleKahn 22 55 20 Input yct-018 FemaleMaxT 18 82.60869565 20 Input yct-019 MaleKahn 16 85 20 Input yct-020 FemaleMaxT 22 85 20 Input yct-021 MaleMaxT 24 81.81818182 20 Input yct-022 FemaleKahn 21 70.83333333 20 Input yct-023 FemaleMaxT 20 52 20 Input yct-024 MaleKahn 16 73.68421053 20 Input yct-025 MaleKahn 21 23.80952381 20 Input yct-026 FemaleMaxT 20 78.26086957 20 Input yct-027 FemaleMaxT 17 20 20 Input yct-030 FemaleMaxT 19 52 20 Input yd-p002 MaleNone 20 54.54545455 10 Input yd-p006 FemaleNone 23 30 10 Input yd-p008 MaleNone 22 44 10 Input yd-p010 FemaleNone 16 50 10 Input yd-p014 FemaleNone 22 3.846153846 10 Input yd-p015 MaleNone 19 10 10 Input yd-p022 FemaleNone 24 37.03703704 10 Input yd-p026 FemaleNone 21 47.61904762 10 Input yd-p027 MaleNone 23 31.57894737 10 Input yd-p032 FemaleNone 21 75 10 Input yd-p033 MaleNone 24 22.22222222 10 Input yd-p034 FemaleNone 22 25 10 Input yd-p035 MaleNone 24 30.43478261 10 Input yd-p047 MaleNone 16 78.26086957 10 Input yd-p048 MaleNone 17 20 10 Input yd-p051 FemaleNone 18 45 10 Input yd-p052 FemaleNone 20 47.82608696 10
3.
0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0
Any help would be greatly appreciated.
Thank you,
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Message: 4 Date: Wed, 14 Oct 2020 13:11:05 +0000 From: Donatas Sederevicius donatas.sederevicius@psykologi.uio.no Subject: [Freesurfer] Reliability and sensitivity of two whole-brain segmentation approaches ? ASEG and SAMSEG To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 2BA6730D-C972-4335-A88C-85CF3C256463@psykologi.uio.no Content-Type: text/plain; charset="utf-8"
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A new pre-print paper comparing two FreeSurfer?s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selection of the processing method.
https://www.biorxiv.org/content/10.1101/2020.10.13.335737v1
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Message: 5 Date: Wed, 14 Oct 2020 15:05:27 +0000 From: "Mcnorgan, Christopher" cpmcnorg@buffalo.edu Subject: [Freesurfer] tk applications failing to launch on VM (Windows) To: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Message-ID: FCD2D972-14C2-4575-8B36-289339860F4F@buffalo.edu Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi, I run Freesurfer remotely on Ubuntu, and locally on my Mac, so I?ve not had this problem personally. Two students are working remotely with PCs and are using the VM installation you folks provided (https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads).
Both of the students report that the tk applications (tkmedit and I think also tksurfer) fail to launch. At the command line, they run the command, and nothing really happens. One student provided a bit more information: I don't know if this helps, but I ran tksurfer and actually got an error that read out, ' TCL_init failed: Cannot find a usable init.tcl. This probably means that Tcl wasn't installed properly. TK_init failed: invalid command name "tcl_find/library? ? Unfortunately I could not provide any help at all because when I attempt to run the VM on virtualbox on my mac, following the directions at https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_mac The OS fails to boot, and I only see a series of messages about recovering a journaled filesystem before the VM halts.
Most of their learning has involved the CLI so it hasn?t been a huge impediment, but we?re about to run the GLM, and will require these resources to visualize.
Thanks, Chris
/********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/
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