The value in the ocn.dat file totally depends on what you used as input (--y) to mri_glmfit. If you used thickness, then it is thickness. That mri_segstats command is almost correct. You will need to add --accumulate so that it gives you the total volume rather than the average
On 06/13/2018 12:47 PM, Hua, Jessica wrote: > > External Email - Use Caution > > Thank you for your response! > > > Just to clarify: if my input is volume, does the > cache.th20.abs.sig.y.ocn.dat contain the average unadjusted volume > values for each participant in each significant cluster? > > > Since the file I just mentioned contains the average values, I used > mri_segstats to calculate total volume for the cluster. > > > mri_segstats --i <pathway to rh.volume.Study.10.mgh> --seg > cache.th20.abs.sig.ocn.mgh --excludeid 0 --sumwf ClusterVolumeValues.dat > > However, this just calculates the sum of the unadjusted values in the > cluster. I guess my main question is, is there a way to extract or > calculate the adjusted values for each participant in each cluster > after accounting for covariates (age, sex, and ICV)? > > > --- > > Jessica > > > ------------------------------------------------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of > freesurfer-requ...@nmr.mgh.harvard.edu > <freesurfer-requ...@nmr.mgh.harvard.edu> > *Sent:* Wednesday, June 13, 2018 11:00 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Freesurfer Digest, Vol 172, Issue 21 > 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-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@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: crypt_gkey = (null) (Dicamillo, Robert) > 2. tractstats2table - all tracts for multiple subjects > (Alexopoulos, Dimitrios) > 3. Re: tractstats2table - all tracts for multiple subjects > (Yendiki, Anastasia) > 4. dwi.ecclog file (Daumail, Loic Jean) > 5. Re: dwi.ecclog file (Yendiki, Anastasia) > 6. Re: tractstats2table - all tracts for multiple subjects > (Alexopoulos, Dimitrios) > 7. Re: Missing Control Points and QATools (Matthew Peverill) > 8. Re: Missing Control Points and QATools (Bruce Fischl) > 9. Re: Extract the entorhinal cortex as a mask (Erik O'Hanlon) > 10. PREDOCTORAL POSITION at King's College London > (Walter Hugo Lopez Pinaya) > 11. Re: Extract the entorhinal cortex as a mask (Bruce Fischl) > 12. Re: "WARNING: Image geometries differ across time" upon > running base step of longitudinal pipeline (Tudor Popescu) > 13. Re: dwi.ecclog file (Daumail, Loic Jean) > 14. Re: Running qcache on old FS data (Douglas N. Greve) > 15. Re: Group Analysis Covariates (Douglas N. Greve) > 16. Re: Error during QDEC (Douglas N. Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 12 Jun 2018 19:52:52 +0000 > From: "Dicamillo, Robert" <rdicami...@mgh.harvard.edu> > Subject: Re: [Freesurfer] crypt_gkey = (null) > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <5024346d-6c53-4e0f-8189-faae089d2...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hello Aaron, > > The build timestamp from the output below shows mri_convert is from > 8/2014. When I look at the build timestamp on our stable 5.3 version > of mri_convert I see it is from 5/2013. So the version that you > listed is about 1 year newer than the 5.3 release I can see. It is > possible that someone downloaded a daily/dev build of freesurfer at > that time. > > You might want to consider running the latest 6.0 release of > Freesurfer (released in January 2017), which should be fine on CentOS > 7. It can be downloaded from, > https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall > > I also suggest that you start out in a default/clean shell, set > FREESURFER_HOME, and then source the setup script for linux, You can > see the instructions on that same web page under ?Setup and > Configuration?. The setup steps should work for version 5 or 6. > > - rob > > On Jun 12, 2018, at 2:43 PM, Aaron Tanenbaum > <aaron.b.tanenb...@gmail.com<mailto:aaron.b.tanenb...@gmail.com>> wrote: > > > External Email - Use Caution > > I checked my system is not encrypted. I had someone else run the > command on the same machine. It worked for them. So I changed my BASH > environment to a default environment. I still get the same error. > > I tried this again but with a different FreeSurfer 5.3. turns out the > one I was using has been altered version of FreeSurfer. I do not know > how it was altered. It worked. so it has to do with the altered > FreeSurfer. > I ran the command mri_convert -version on both FreeSurfer. > > for the unaltered i get the out put > mri_convert -version > stable5 > altered version i get > mri_convert -version > dev build (use --all-info flag for full version info) > > with this output i type in mri_convert --all-info > mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ > TimeStamp: 2018/06/12-18:32:17-GMT BuildTimeStamp: Aug 22 2014 > 21:04:47 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl > Exp $ User: tanenbauma Machine: rocky Platform: Linux > PlatformVersion: 3.10.0-862.el7.x86_64 CompilerName: GCC > CompilerVersion: 40400 > Wondering is this version of mri_convert a developmental version? > Also both version are the CentOS 6 build. > > > On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert > <rdicami...@mgh.harvard.edu<mailto:rdicami...@mgh.harvard.edu>> wrote: > Hello Aaron, > > You could check to see if the CentOS 7 system is using disk > encryption, e.g., if the > following command return 1, then it would mean encryption is in use > (which can be > an issue with FreeSurfer). > > $ cat /proc/sys/crypto/fips_enabled > > If it returns zero, it could be an issue with a system library like > glibc on CentOS 7.5 > (that does not happen on older versions of CentOS). > > Either way, this is not your doing ;-) > > > On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum > <aaron.b.tanenb...@gmail.com<mailto:aaron.b.tanenb...@gmail.com>> wrote: > > > External Email - Use Caution > > I am currently running CentOS 7.5 and attempting to run FreeSurfer > 5.3. When i get to the part where MRI_convert is creating the the > orig001.mgz its gives me a segmentation fault. if i run this on a > centos 6 system it works fine. below is the output of the program. > > > /data/gizmo/data1/freesurfer5.3/bin/mri_convert > /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm > > /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz > $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ > reading from > /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm... > crypt_gkey = (null) > Segmentation fault (core dumped) > > > > Did I do anything wrong? > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@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@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180612/b22dc55d/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Tue, 12 Jun 2018 21:08:20 +0000 > From: "Alexopoulos, Dimitrios" <dimitriosalexopou...@wustl.edu> > Subject: [Freesurfer] tractstats2table - all tracts for multiple > subjects > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <cy1pr0201mb1914d2cdcde64f2a2093ac89d6...@cy1pr0201mb1914.namprd02.prod.outlook.com> > > Content-Type: text/plain; charset="us-ascii" > > External Email - Use Caution > > Hi, > > > For a group analysis, it possible to use 'tractstats2table' to > generate a single table that contains all the tracts for multiple > subjects? > > > > It's not intuitively obvious looking at the options with the > 'tractstats2table' utility. > > > > Jim > > > "The materials in this email are private and may contain Protected > Health Information. If you are not the intended recipient, be advised > that any unauthorized use, disclosure, copying, distribution or the > taking of any action in reliance on the contents of this information > is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return email." > > > ________________________________ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180612/eeb60af9/attachment-0001.html > > > > ------------------------------ > > Message: 3 > Date: Tue, 12 Jun 2018 21:30:05 +0000 > From: "Yendiki, Anastasia" <ayend...@mgh.harvard.edu> > Subject: Re: [Freesurfer] tractstats2table - all tracts for multiple > subjects > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <blupr0401mb1713489d7ce131b99d103eed8a...@blupr0401mb1713.namprd04.prod.outlook.com> > > Content-Type: text/plain; charset="windows-1252" > > Hi Jim - You can use the --load-pathstats-from-file option, as in the > tutorial, to pass a text file that contains the paths to all the stats > files that you want to include in the table. These can be from > multiple subjects and/or tracts. > > > http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics > > > Best, > > a.y > > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alexopoulos, > Dimitrios <dimitriosalexopou...@wustl.edu> > Sent: Tuesday, June 12, 2018 5:08:20 PM > To: Freesurfer support list > Subject: [Freesurfer] tractstats2table - all tracts for multiple subjects > > > External Email - Use Caution > > Hi, > > > > For a group analysis, it possible to use ?tractstats2table? to > generate a single table that contains all the tracts for multiple > subjects? > > > > It?s not intuitively obvious looking at the options with the > ?tractstats2table? utility. > > > > Jim > > > > > > ?The materials in this email are private and may contain Protected > Health Information. If you are not the intended recipient, be advised > that any unauthorized use, disclosure, copying, distribution or the > taking of any action in reliance on the contents of this information > is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return email.? > > > > > > ________________________________ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180612/8afd6caf/attachment-0001.html > > > > ------------------------------ > > Message: 4 > Date: Tue, 12 Jun 2018 21:33:17 +0000 > From: "Daumail, Loic Jean" <ldaum...@mgh.harvard.edu> > Subject: [Freesurfer] dwi.ecclog file > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <f1dcee78c79e7046ac0b5ba33993892801009...@phsx10mb2.partners.org> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > I have several questions regarding the dwi.ecclog file data from > Tracula, using the FreeSurfer version V6.0.0. > > 1) Does Tracula still use eddy_correct from FSL, or was it updated > with the new eddy function from FSL? > > 2) Are the values for each slice of dwi.ecclog relative to the first > slice or to the previous slice, or to another template? is it the same > for both rotation and translation values? > > 3) What is the coordinate system for the rotation values? Is there a > way to determine the total rotation from these 9 values? > > Thanks, > > Sincerely, > > Loic Daumail > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180612/91e47f66/attachment-0001.html > > > > ------------------------------ > > Message: 5 > Date: Tue, 12 Jun 2018 21:40:17 +0000 > From: "Yendiki, Anastasia" <ayend...@mgh.harvard.edu> > Subject: Re: [Freesurfer] dwi.ecclog file > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <blupr0401mb1713fb9bd0ad965d70f7272b8a...@blupr0401mb1713.namprd04.prod.outlook.com> > > Content-Type: text/plain; charset="us-ascii" > > Hi Loic - The command that computes the motion measures is > dmri_motion, and it can take either the eddy_correct or eddy format as > input. The former format contains affine registration matrices with > respect to the reference frame (which usually is the first b=0). The > latter format contains the shift/rotation/etc. parameters of the > registration rather than the matrix itself. You can run dmri_motion > without arguments to see details. > > > Best, > > a.y > > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daumail, Loic > Jean <ldaum...@mgh.harvard.edu> > Sent: Tuesday, June 12, 2018 5:33:17 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] dwi.ecclog file > > Hello, > > I have several questions regarding the dwi.ecclog file data from > Tracula, using the FreeSurfer version V6.0.0. > > 1) Does Tracula still use eddy_correct from FSL, or was it updated > with the new eddy function from FSL? > > 2) Are the values for each slice of dwi.ecclog relative to the first > slice or to the previous slice, or to another template? is it the same > for both rotation and translation values? > > 3) What is the coordinate system for the rotation values? Is there a > way to determine the total rotation from these 9 values? > > Thanks, > > Sincerely, > > Loic Daumail > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180612/f7d50410/attachment-0001.html > > > > ------------------------------ > > Message: 6 > Date: Tue, 12 Jun 2018 21:50:59 +0000 > From: "Alexopoulos, Dimitrios" <dimitriosalexopou...@wustl.edu> > Subject: Re: [Freesurfer] tractstats2table - all tracts for multiple > subjects > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <cy1pr0201mb191466973da1b7223811faa0d6...@cy1pr0201mb1914.namprd02.prod.outlook.com> > > Content-Type: text/plain; charset="us-ascii" > > External Email - Use Caution > > Thx Anastasia. > > This the command I used and the error: > > [hellerml@login01 processed_data]$ tractstats2table > --load-pathstats-from-file > /scratch/jimalex/freesurfer6_0_chd_auck_6yr/processed_data/test.list > --overall --tablefile test.table > Parsing the .stats files > Building the table.. > ERROR: all stats files need to have the same pathwayname. try verbose > option > These are the pathwaynames found: ['fmajor', 'fminor', 'lh.atr', > 'lh.cab', 'lh.ccg', 'lh.cst', 'lh.ilf', 'lh.slfp', 'lh.slft', > 'lh.unc', 'rh.atr', 'rh.cab', 'rh.ccg', 'rh.cst', 'rh.ilf', 'rh.slfp', > 'rh.slft', 'rh.unc'] > > For example, the test .list input file I used for a single subject is > below: > -------------------------------- > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/fminor_PP_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.atr_PP_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.cab_PP_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.ccg_PP_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.slft_PP_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.unc_AS_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.atr_PP_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.cab_PP_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.ccg_PP_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.cst_AS_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.slft_PP_avg33_mni_bbr/pathstats.overall.txt > $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt > > > > "The materials in this email are private and may contain Protected > Health Information. If you are not the intended recipient, be advised > that any unauthorized use, disclosure, copying, distribution or the > taking of any action in reliance on the contents of this information > is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return email." > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, > Anastasia > Sent: Tuesday, June 12, 2018 4:30 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] tractstats2table - all tracts for multiple > subjects > > > Hi Jim - You can use the --load-pathstats-from-file option, as in the > tutorial, to pass a text file that contains the paths to all the stats > files that you want to include in the table. These can be from > multiple subjects and/or tracts. > > > > http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics > > > > Best, > > a.y > > ________________________________ > From: > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > > on behalf of Alexopoulos, Dimitrios > <dimitriosalexopou...@wustl.edu<mailto:dimitriosalexopou...@wustl.edu>> > Sent: Tuesday, June 12, 2018 5:08:20 PM > To: Freesurfer support list > Subject: [Freesurfer] tractstats2table - all tracts for multiple subjects > > > External Email - Use Caution > > Hi, > > > > For a group analysis, it possible to use 'tractstats2table' to > generate a single table that contains all the tracts for multiple > subjects? > > > > It's not intuitively obvious looking at the options with the > 'tractstats2table' utility. > > > > Jim > > > > > > "The materials in this email are private and may contain Protected > Health Information. If you are not the intended recipient, be advised > that any unauthorized use, disclosure, copying, distribution or the > taking of any action in reliance on the contents of this information > is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return email." > > > > > > ________________________________ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > > ________________________________ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180612/e32cefa8/attachment-0001.html > > > > ------------------------------ > > Message: 7 > Date: Tue, 12 Jun 2018 18:07:17 -0700 > From: Matthew Peverill <mrpever...@gmail.com> > Subject: Re: [Freesurfer] Missing Control Points and QATools > To: freesurfer <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CABnnpkMeW5ZrtszCDSz99=jbs1+jvqwylipqgb8h+5nt0ka...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi all, > Sorry for the bump but I wanted to take one more shot at this. We're > making > it back but we've lost many, many hours of editing work. Has anyone else > had experiences with QAtools, or other FreeSurfer utilities, removing > control point data, or discovered any way to recover control.dat from > other > files? Thank you, > -Matt > > On Mon, May 21, 2018 at 11:35 AM Matthew Peverill <mrpever...@gmail.com> > wrote: > > > Hello, > > We are finishing up manual inspection and editing of our dataset. As > part > > of this process, we used QATools to generate QA reports. While we were > > running our reports the tmp/control.dat file was deleted from many > of our > > subject directories (the brains had already been recon'd, so the > corrected > > surfaces were not affected). The timing certainly suggests these were > > related, but we have no way of knowing if something else unrelated to > > QAtools happened that caused these files to be deleted. So two > questions: > > > > 1) Has anyone else had an experience with QAtools where the control.dat > > file was deleted, or have any insight about why this could have > happened? > > 2) Is the data in control.dat stored anywhere else? For example, can > it be > > recovered from mri/ctrl_pts.mgz? We are mostly fine, but a few > brains will > > need to have control points re-applied. > > > > Something of a shot in the dark, but we would love any suggestions. > Thanks, > > -Matt > > > > Version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > uname -a: Linux vmpfc 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1+deb8u2 > > (2017-03-07) x86_64 GNU/Linux > > > > > > -- > > Matthew Peverill > > mrpever...@gmail.com (preferred) > > > > > -- > Matthew Peverill > 857-277-9083 > mrpever...@gmail.com (preferred) > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180612/6089d1c3/attachment-0001.html > > > > ------------------------------ > > Message: 8 > Date: Tue, 12 Jun 2018 21:17:42 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Missing Control Points and QATools > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1806122114340.32...@gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Matt > > I'm sorry to hear it. I've never heard of anything of ours deleting the > control.dat unless you run recon-all with the appropriate -clean switch. > > I don't know an easy way to recover them. Do you need them back? You could > do something like copy the subject, run the intensity normalization on > the > copy, then look for points that are exactly 110 in the old > (control-point-normalized) brain.mgz and the new one without control > points, that are also wm in the aseg.mgz. This won't be exactly the > control > points, but would let you rerun without losing too much if that is > what you > are worried about > > cheers > Bruce > > > > On Tue, 12 Jun 2018, Matthew Peverill wrote: > > > > > ????????External Email - Use Caution???????? > > > > Hi all,Sorry for the bump but I wanted to take one more shot at > this. We're making it back but we've > > lost many, many hours of editing work. Has anyone else had > experiences with QAtools, or other > > FreeSurfer utilities, removing control point data, or discovered any > way to recover control.dat from > > other files? Thank you, > > ? ?-Matt > > > > On Mon, May 21, 2018 at 11:35 AM Matthew Peverill > <mrpever...@gmail.com> wrote: > > Hello, > > We are finishing up manual inspection and editing of our > dataset. As part of this > > process, we used QATools to generate QA reports. While we were > running our reports the > > tmp/control.dat file was deleted from many of our subject > directories (the brains had > > already been recon'd, so the corrected surfaces were not > affected). The timing certainly > > suggests these were related, but we have no way of knowing if > something else unrelated > > to QAtools happened that caused these files to be deleted. So > two questions: > > > > 1) Has anyone else had an experience with QAtools where the > control.dat file was deleted, or > > have any insight about why this could have happened? > > 2) Is the data in control.dat stored anywhere else? For example, can > it be recovered > > from?mri/ctrl_pts.mgz? We are mostly fine, but a few brains will > need to have control points > > re-applied. > > > > Something of a shot in the dark, but we would love any suggestions. > Thanks, > > ? ?-Matt > > > > Version:?freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > uname -a:?Linux vmpfc 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1+deb8u2 > (2017-03-07) x86_64 > > GNU/Linux > > > > > > -- > > Matthew Peverill > > mrpever...@gmail.com (preferred) > > > > > > > > -- > > Matthew Peverill > > 857-277-9083 > > mrpever...@gmail.com (preferred) > > > > > > ------------------------------ > > Message: 9 > Date: Wed, 13 Jun 2018 11:19:38 +0000 > From: "Erik O'Hanlon" <erikohan...@rcsi.ie> > Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <am0pr07mb4209cf0074f152a501ecf7c8a3...@am0pr07mb4209.eurprd07.prod.outlook.com> > > Content-Type: text/plain; charset="us-ascii" > > External Email - Use Caution > > Sorry Bruce, > > > Yep Thanks. I didn't spot that label just the 216. Worked perfectly. > > > Thanks again > > > Erik > > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > Sent: 12 June 2018 19:04:32 > To: Freesurfer support list > Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask > > I think you can use 1006 (left) and 2006 (right) > > cheers > Bruce > On Tue, 12 Jun 2018, Erik > O'Hanlon wrote: > > > External Email - Use Caution > > > > Hi Bruce, > > > > > > Thanks. So if I use the following command > > > > mri_extract_Label aparc+aseg.mgz 216 EC.mgz > > > > would that give me both L and right EC extracted? is there any way > to get the left and right separately? > > > > > > Thanks so much for the help > > > > > > cheers > > > > > > Erik > > > > Erik O'Hanlon > Postdoctoral researcher > > [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] > > RCSI Psychiatry > Royal College of Surgeons in Ireland > Beaumont Road, Beaumont D9 Ireland > T: 8093740 > E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> > > > Transforming Healthcare Education, Research and Service: RCSI > Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> > > > RCSI LEADING THE WORLD TO BETTER HEALTH > > [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] > > > > ________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > > Sent: 12 June 2018 14:56:41 > > To: Freesurfer support list > > Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask > > > > Hi Erik > > > > yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC > > as a volume mask > > > > cheers > > Bruce > > On Tue, 12 Jun 2018, Erik O'Hanlon wrote: > > > >> External Email - Use Caution > >> > >> Hi FS experts , > >> > >> > >> I'd like to make masks for the entorhinal cortex to use for > tractography. Can you advise what FS tool should be used? I've used > the mri_extract_label for my hippocampal masks but not sure what files > to use to extract EC ? I'm sure it's straightforward > >> > >> > >> Thanks for any advice > >> > >> > >> Best regards > >> > >> > >> Erik > >> > >> Erik O'Hanlon > >> Postdoctoral researcher > >> > >> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] > >> > >> RCSI Psychiatry > >> Royal College of Surgeons in Ireland > >> Beaumont Road, Beaumont D9 Ireland > >> T: 8093740 > >> E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> > >> > >> > >> Transforming Healthcare Education, Research and Service: RCSI > Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> > >> > >> > >> RCSI LEADING THE WORLD TO BETTER HEALTH > >> > >> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > 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 > <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. > > > > > > Erik O'Hanlon > > Postdoctoral researcher > > > > [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] > > > > RCSI Psychiatry > > Royal College of Surgeons in Ireland > > Beaumont Road, Beaumont D9 Ireland > > T: 8093740 > > E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> > > > > > > Transforming Healthcare Education, Research and Service: RCSI > Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> > > > > > > RCSI LEADING THE WORLD TO BETTER HEALTH > > > > [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180613/f1a5e889/attachment-0001.html > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png > Type: image/png > Size: 8772 bytes > Desc: rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180613/f1a5e889/attachment-0002.png > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png > Type: image/png > Size: 16296 bytes > Desc: both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180613/f1a5e889/attachment-0003.png > > > > ------------------------------ > > Message: 10 > Date: Wed, 13 Jun 2018 12:57:38 +0100 > From: Walter Hugo Lopez Pinaya <walhug...@gmail.com> > Subject: [Freesurfer] PREDOCTORAL POSITION at King's College London > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CAN7TPXWEP4ywrZBPa3VVwkwH07YrGGC+d=FHQD=tjd-4pgg...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Dear colleagues, > > > We are looking for a predoctoral research assistant with knowledge of > neuroimaging to work on a research project involving the application of > machine learning techniques to neuroanatomical data. > > The project will lead to the development of a practical and flexible > web-based tool for measuring neuroanatomical alterations in any > brain-based > disorders. > > The successful applicant will have previous experience in the handling of > multiple structural neuroimaging datasets within the same project. > Previous > experience of using machine learning would be considered a strength but is > not a requisite. The post holder will join a multi-disciplinary team > including neuroscientists, psychologists and computer scientists. > > This project is a collaboration between King?s College London, UK (Dr. > Andrea Mechelli), the University of New Mexico, USA (Prof. Vince Calhoun) > and the Universidade Federal do ABC, Brazil (Prof Jo?o Sato) and is funded > by an Innovator Award from the Wellcome Trust. The post holder will be > based at the Institute of Psychiatry, Psychology & Neuroscience (King?s > College London). > > > For more information, please see > https://www.hirewire.co.uk/HE/1061247/MS_JobDetails.aspx?JobID=79233 > > Best wishes, > > Walter Hugo Diaz Sanz > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180613/3999dc7f/attachment-0001.html > > > > ------------------------------ > > Message: 11 > Date: Wed, 13 Jun 2018 09:45:50 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1806130945470.12...@gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > glad to hear it > Bruce > On Wed, 13 Jun 2018, Erik O'Hanlon wrote: > > > External Email - Use Caution > > > > Sorry Bruce, > > > > > > Yep Thanks. I didn't spot that label just the 216. Worked perfectly. > > > > > > Thanks again > > > > > > Erik > > > > ________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > > Sent: 12 June 2018 19:04:32 > > To: Freesurfer support list > > Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask > > > > I think you can use 1006 (left) and 2006 (right) > > > > cheers > > Bruce > > On Tue, 12 Jun 2018, Erik > > O'Hanlon wrote: > > > >> External Email - Use Caution > >> > >> Hi Bruce, > >> > >> > >> Thanks. So if I use the following command > >> > >> mri_extract_Label aparc+aseg.mgz 216 EC.mgz > >> > >> would that give me both L and right EC extracted? is there any way > to get the left and right separately? > >> > >> > >> Thanks so much for the help > >> > >> > >> cheers > >> > >> > >> Erik > >> > > > > Erik O'Hanlon > > Postdoctoral researcher > > > > [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] > > > > RCSI Psychiatry > > Royal College of Surgeons in Ireland > > Beaumont Road, Beaumont D9 Ireland > > T: 8093740 > > E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> > > > > > > Transforming Healthcare Education, Research and Service: RCSI > Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> > > > > > > RCSI LEADING THE WORLD TO BETTER HEALTH > > > > [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] > > > > > >> ________________________________ > >> From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > >> Sent: 12 June 2018 14:56:41 > >> To: Freesurfer support list > >> Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask > >> > >> Hi Erik > >> > >> yes, you can apply mri_extract_label to the aparc+aseg.mgz to > extract EC > >> as a volume mask > >> > >> cheers > >> Bruce > >> On Tue, 12 Jun 2018, Erik O'Hanlon wrote: > >> > >>> External Email - Use Caution > >>> > >>> Hi FS experts , > >>> > >>> > >>> I'd like to make masks for the entorhinal cortex to use for > tractography. Can you advise what FS tool should be used? I've used > the mri_extract_label for my hippocampal masks but not sure what files > to use to extract EC ? I'm sure it's straightforward > >>> > >>> > >>> Thanks for any advice > >>> > >>> > >>> Best regards > >>> > >>> > >>> Erik > >>> > >>> Erik O'Hanlon > >>> Postdoctoral researcher > >>> > >>> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] > >>> > >>> RCSI Psychiatry > >>> Royal College of Surgeons in Ireland > >>> Beaumont Road, Beaumont D9 Ireland > >>> T: 8093740 > >>> E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> > >>> > >>> > >>> Transforming Healthcare Education, Research and Service: RCSI > Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> > >>> > >>> > >>> RCSI LEADING THE WORLD TO BETTER HEALTH > >>> > >>> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] > >>> > >>> > >> _______________________________________________ > >> Freesurfer mailing list > >> 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 > <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. > >> > >> > >> Erik O'Hanlon > >> Postdoctoral researcher > >> > >> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] > >> > >> RCSI Psychiatry > >> Royal College of Surgeons in Ireland > >> Beaumont Road, Beaumont D9 Ireland > >> T: 8093740 > >> E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> > >> > >> > >> Transforming Healthcare Education, Research and Service: RCSI > Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> > >> > >> > >> RCSI LEADING THE WORLD TO BETTER HEALTH > >> > >> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 12 > Date: Wed, 13 Jun 2018 16:34:58 +0200 > From: Tudor Popescu <tud...@gmail.com> > Subject: Re: [Freesurfer] "WARNING: Image geometries differ across > time" upon running base step of longitudinal pipeline > To: free surfer <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <cagbir40vnfk6ztxb7byhx5qf_wumrhja4qkvzdwebf8okl0...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Bruce, > > I am guessing that Martin might be unavailable for now, judging by the > date > of his last input to the list. > > However, my intuition is that there is something really trivial that's > causing this chain of (circular!) errors... > > For any more ideas of what I could try, I'd remain really indebted! > > Cheers, > Tudor > > On Mon, 11 Jun 2018 at 16:03, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > > > Hi Tudor > > > > I think Martin is probably better able to sort this out than I am. > > > > Bruce > > > > > > On Mon, 11 Jun 2018, Tudor Popescu wrote: > > > > > > > > External Email - Use Caution > > > > > > Hi Bruce, > > > I assumed a subject-specific target for the mri_convert, so I used > this > > command to realign > > > subject1's post to his pre: > > > mri_convert -rl 01_1.nii.gz 01_2.nii.gz 01_2resampled.nii.gz > > > > > > (and renamed the resampled file to 01_2). However, then the base step > > > recon-all -base 01 -tp 01_1 -tp 01_2 -all > > > > > > still gives the same warning about geometries differing across > time; and > > also in addition, this > > > error message (which might have been there earlier too but had gone > > unnoticed): > > > mghRead(/media/FS/01_1/mri/norm.mgz, -1): could not open file > > > MultiRegistration::loadMovables: could not open input volume > > /media/FS/01_1/mri/norm.mgz. > > > > > > Inside /media/FS/01_1/mri/ (where /media/FS is my $SUBJECTS_DIR), > there > > is indeed no norm.mgz, which > > > suggests something in my previous commands: > > > recon-all -i 01_1.nii.gz -subjid 01_1 > > > recon-all -i 01_2.nii.gz -subjid 01_2 > > > recon-all -subjid 01_1 -all > > > recon-all -subjid 01_2 -all > > > > > > ..has gone wrong despite these having produced no errors. Although I > > thought the base step already > > > does autorecon1 as part of the longitudinal pipeline, I tried doing it > > manually: > > > recon-all -autorecon1 -subjid 01 > > > > > > however this returns: > > > ERROR: It appears that this subject ID is an existing > > base/template from longitudinal > > > processing (-base). Please make sure you pass all necessary > flags. > > For example, if you > > > are trying to re-run a -base: \' -base <templateid> -tp <tpNid> > > ... \' > > > > > > ..and running autorecon1 and 2 for the first timepoint instead, > > > recon-all -autorecon1 -autorecon2 -subjid 01_1 > > > > > > returns > > > mri_em_register: could not open input volume nu.mgz > > > > > > > > > Not sure what to do at this stage!.. Thanks again for any pointers! > > > > > > Cheers, > > > Tudor > > > > > > On Thu, 7 Jun 2018 at 18:16, Tudor Popescu <tud...@gmail.com> wrote: > > > Hi Bruce, > > > Thanks for your answer! Before seeing this warning (rather: error, > as no > > output is produced), > > > I'd not have thought the pre-post images have different geometries, as > > I'm pretty sure their > > > acquisition parameters were the same. The pre and post of any one > > subject, as well as the > > > different subjects' images, all seem to have identical voxel size > > (1x1x1) and image size > > > (176x224x160). Furthemore, the (0,0,0) point seems to always overlap > > well-enough on the > > > anterior commissure... > > > > > > This all suggests to me the geometry differences are trivial, so the > > resampling is worth a > > > try. However, I'm unsure whether, in the call to mri_convert -rl, the > > target would have to > > > be subject-specific (e.g. resample each 'post' to the 'pre' baseline), > > or if I should use a > > > single target for all the pre&post images in the study, a bit like the > > study-specific template > > > used by VBM? > > > > > > Cheers, > > > Tudor > > > > > > > > > > > > On 6 June 2018 at 16:37, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > > wrote: > > > Hi Tudor > > > > > > if you are sure that the differences are trivial you can > resample > > the images to > > > all have exactly the same geometries and rerun (I think > > mri_convert -rl <target > > > vol> <source vol> <source vol resampled> > > > > > > should do it (-rl is "reslice like"). If they are not trivial > > though you may find > > > effects that only reflect the acquisition differences. > > > > > > cheers > > > Bruce > > > > > > On Wed, 6 Jun 2018, Tudor Popescu wrote: > > > > > > > > > External Email - Use Caution > > > > > > Hello, > > > If any more information is needed to address my question, > > please do > > > let me know. I hope to hear back and once again > > > thanks a lot for any assistance with this. > > > > > > Best wishes, > > > Tudor > > > > > > On 1 June 2018 at 16:07, Tudor Popescu <tud...@gmail.com> > > wrote: > > > Dear all, > > > I have pre and post-intervention data for a single > group of > > subjects, > > > and I'd like to extract the cortical > > > thickness pre and post, for all standard regions in the > > atlas, and use > > > those in subsequent analyses. > > > > > > Following the standard approach for longitudinal > studies, I > > used the > > > following types of commands: > > > 1. recon-all -i 01_1.nii.gz -subjid 01_1 > > > recon-all -i 01_2.nii.gz -subjid 01_2 > > > recon-all -i 02_1.nii.gz -subjid 02_1 > > > .. > > > where e.g. 01 is the subj code, and _1 and _2 > represent > > pre and > > > post scans > > > 2. recon-all -subjid 01_1 -all > > > recon-all -subjid 01_2 -all > > > .. > > > 3. recon-all -base 01 -tp 01_1 -tp 01_2 -all > > > .. > > > 4. recon-all -long 01_1 01 -all > > > recon-all -long 01_2 01 -all > > > .. > > > However, the base step has led to warnings of the type: > > "WARNING: > > > Image geometries differ across time, maybe > > > due to aquisition changes? This can potentially bias a > > longitudinal > > > study! ", and consequently to an empty > > > /stats folder -- even though my pre and post images are > > aligned and > > > have similar acquisition parameters. > > > > > > Have I done something wrong, and how can I fix this > > warning/error? > > > Many thanks in advance for any help. > > > > > > Best wishes, > > > Tudor > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > 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 > <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@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 > <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. > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180613/9b9e4135/attachment-0001.html > > > > ------------------------------ > > Message: 13 > Date: Wed, 13 Jun 2018 15:09:11 +0000 > From: "Daumail, Loic Jean" <ldaum...@mgh.harvard.edu> > Subject: Re: [Freesurfer] dwi.ecclog file > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <f1dcee78c79e7046ac0b5ba33993892801009...@phsx10mb2.partners.org> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Mrs Yendiki, > > thank you for your response. > However, for my configuration file, containing : > " > setenv SUBJECTS_DIR > /autofs/space/avadhuti_001/users/gdesbord/CALM_data/CALM_001 > > set subjlist = ( 02_recon ) > > set dcmlist = ( > /autofs/space/avadhuti_001/users/gdesbord/CALM_data/Qball_data/raw_DICOMs/CALM_001/02/892000-000015-000001.dcm) > > set doeddy = 1 > > set dorotbvecs = 1 > > " > > Did "doeddy = 1" use eddy_correct or eddy format? > Also, I am not sure about the units, is it in mm and degrees for the > values in dwi.ecclog file? > > Thank you, > > Sincerely, > > Loic > > > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, > Anastasia [ayend...@mgh.harvard.edu] > Sent: Tuesday, June 12, 2018 5:40 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] dwi.ecclog file > > > Hi Loic - The command that computes the motion measures is > dmri_motion, and it can take either the eddy_correct or eddy format as > input. The former format contains affine registration matrices with > respect to the reference frame (which usually is the first b=0). The > latter format contains the shift/rotation/etc. parameters of the > registration rather than the matrix itself. You can run dmri_motion > without arguments to see details. > > > Best, > > a.y > > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daumail, Loic > Jean <ldaum...@mgh.harvard.edu> > Sent: Tuesday, June 12, 2018 5:33:17 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] dwi.ecclog file > > Hello, > > I have several questions regarding the dwi.ecclog file data from > Tracula, using the FreeSurfer version V6.0.0. > > 1) Does Tracula still use eddy_correct from FSL, or was it updated > with the new eddy function from FSL? > > 2) Are the values for each slice of dwi.ecclog relative to the first > slice or to the previous slice, or to another template? is it the same > for both rotation and translation values? > > 3) What is the coordinate system for the rotation values? Is there a > way to determine the total rotation from these 9 values? > > Thanks, > > Sincerely, > > Loic Daumail > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180613/25a6677a/attachment-0001.html > > > > ------------------------------ > > Message: 14 > Date: Wed, 13 Jun 2018 11:20:16 -0400 > From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Running qcache on old FS data > To: <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <6877f84e-1e94-65f2-3de6-e66c96774...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8"; format=flowed > > I have no idea how to make it work with data that old. You can "fool" it > by copying or soft linking lh.curv to lh.white.K. You can probably get > it to at least finish. > > > On 06/06/2018 03:41 PM, Jamie Hanson wrote: > > > > ????????External Email - Use Caution > > > > > > Hello all, > > > > I was trying to run?qcache?on some previously processed Freesurfer > > data from a colleague, but ran into some issues with missing files and > > wondered how best to proceed. > > > > Details: > > -The data was processed with (Freesurfer) v4.5.0 and I would ideally > > like to not reprocess it with a newer version (to keep in concordance > > with past published work, and also it's a large number of subjects, > > n=800+). > > -The qcache flag was not used with the data previously (to my > > knowledge), so I was attempting to run this command: recon-all -s > > $subj -qcache > > -When I try that command, I get an error regarding a > > missing?lh.white.K file. > > > > I've uploaded the log file here: > > https://www.dropbox.com/s/94mnsy7wrps5ce2/recon-all.log?dl=0 > > > > I wondered if it was possible to complete qcache with the data as is? > > I searched on the list previously and saw one or two other folks had > > run into this issues; I, however, didn't see a final solution to > > things. Any thoughts or suggestions are greatly appreciated! Thanks > much! > > > > Best, > > Jamie. > > > > -- > > Jamie Hanson > > Assistant Professor, Psychology > > Research Scientist, Learning Research and Development Center > > University of Pittsburgh > > Personal website: jamiehanson.org <http://jamiehanson.org> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 15 > Date: Wed, 13 Jun 2018 11:52:52 -0400 > From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Group Analysis Covariates > To: <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <fe0de347-e3a3-2c18-af56-47dc48e9e...@mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252"; format=flowed > > > > On 06/11/2018 11:07 PM, Hua, Jessica wrote: > > > > > > Dear Freesurfer Experts: > > > > > > I analyzed my data following the guidelines on the FSL Tutorial/Group > > Analysis page . I am trying to plot the adjusted values (covariates: > > age, sex, and ICV)?for the significant clusters for each of my > > participants. > > > I assume you mean FreeSurfer, not FSL? > > > > > > I set up the contrast to test group differences. So testing whether > > there is a difference between groups regressing out the effects of > > sex, age, and ICV. Contrasts?created were? [1 -1 0 0 0 0 0 0] and [-1 > > 1 0 0 0 0 0 0]. > > > > > > I?then extracted values from this file > > (cache.th20.abs.sig.y.ocn.dat;?i.e., the average value of each subject > > in each cluster) into my dataset. I believe these are the unadjusted > > values, correct? > > > These are the average thickness data (assuming you are using thickness > as input --y) > > > > I calculated total volume and total surface area by multiplying these > > values by the total number of vertices in each cluster. > > > Not sure what you mean here or how it works. > > > > To adjust for covariates, I ran a regression with the > > ExtractedClusterValues as the DV and?Group, Sex, Age, and ICV as > > predictors. Looking at the output, there was no significant effect of > > group (p = .769; whereas in FreeSurfer the cluster-wise p < .001). > > > What were you using to do this test? You really need to have exactly the > same design matrix and contrast matrix. > > > > Also when I plotted the predicted values adjusting for covariates, the > > means between the groups were very similar. > > > > > > Why am I getting a p = .769 when I adjust for covariates, but > > FreeSurfer has a cluster-wise p < .001? Or is there a way to calculate > > adjusted values in FreeSurfer? > > > > > > Best, > > > > > > Jessica > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 16 > Date: Wed, 13 Jun 2018 11:54:08 -0400 > From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Error during QDEC > To: <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <c755a260-8d08-eb9c-91a2-b17f6df17...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8"; format=flowed > > can you send the fsgd file? > > > On 06/12/2018 02:32 AM, Seung-Gul Kang (???) wrote: > > Dear Freesurfer experts, > > > > I see the error message when I perform QDEC. > > The error message is as below. > > > > Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > > > > cwd /home/sgk > > > > cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods > > --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh > > --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C > > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > > > > sysnameLinux > > > > hostname localhost.localdomain > > > > machinex86_64 > > > > usersgk > > > > FixVertexAreaFlag = 1 > > > > UseMaskWithSmoothing1 > > > > OneSampleGroupMean 0 > > > > y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > > > logyflag 0 > > > > usedti0 > > > > FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd > > > > labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label > > > > maskinv 0 > > > > glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > > > IllCondOK 0 > > > > ReScaleX 1 > > > > DoFFx 0 > > > > Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > > > Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > > > INFO: gd2mtx_method is dods > > > > Saving design matrix to /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat > > > > Normalized matrix condition is 24522.5 > > > > Design matrix ------------------ > > > > > 1.0000.0000.0000.00015.0000.0000.0000.00024.0000.0000.0000.00021.0000.0000.0000.000149457.5940.0000.0000.000; > > > > > 1.0000.0000.0000.00019.0000.0000.0000.00050.0000.0000.0000.00020.0000.0000.0000.000161540.2030.0000.0000.000; > > > > > 1.0000.0000.0000.0007.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000167295.9060.0000.0000.000; > > > > > 0.0000.0001.0000.0000.0000.00010.0000.0000.0000.00031.0000.0000.0000.00027.0000.0000.0000.000175241.7030.000; > > > > > 0.0000.0001.0000.0000.0000.00015.0000.0000.0000.00059.0000.0000.0000.00023.0000.0000.0000.000165616.7970.000; > > > > > 0.0000.0001.0000.0000.0000.00011.0000.0000.0000.00057.0000.0000.0000.00022.0000.0000.0000.000183255.5940.000; > > > > > 1.0000.0000.0000.00026.0000.0000.0000.00037.0000.0000.0000.00023.0000.0000.0000.000159212.2030.0000.0000.000; > > > > > 0.0000.0001.0000.0000.0000.00014.0000.0000.0000.00050.0000.0000.0000.00022.0000.0000.0000.000170017.0940.000; > > > > > 0.0000.0001.0000.0000.0000.00016.0000.0000.0000.00026.0000.0000.0000.00019.0000.0000.0000.000190217.9060.000; > > > > > 0.0000.0001.0000.0000.0000.0001.0000.0000.0000.00039.0000.0000.0000.00019.0000.0000.0000.000156341.0000.000; > > > > > 1.0000.0000.0000.00018.0000.0000.0000.00049.0000.0000.0000.00032.0000.0000.0000.000168844.2970.0000.0000.000; > > > > > 1.0000.0000.0000.00021.0000.0000.0000.00039.0000.0000.0000.00026.0000.0000.0000.000149945.4060.0000.0000.000; > > > > > 1.0000.0000.0000.00011.0000.0000.0000.00039.0000.0000.0000.00022.0000.0000.0000.000166132.9060.0000.0000.000; > > > > > 1.0000.0000.0000.00017.0000.0000.0000.00041.0000.0000.0000.00025.0000.0000.0000.000139924.4060.0000.0000.000; > > > > > 1.0000.0000.0000.00027.0000.0000.0000.00045.0000.0000.0000.00034.0000.0000.0000.000133331.7970.0000.0000.000; > > > > > 1.0000.0000.0000.00011.0000.0000.0000.00047.0000.0000.0000.00024.0000.0000.0000.000164844.7030.0000.0000.000; > > > > > 1.0000.0000.0000.00023.0000.0000.0000.00046.0000.0000.0000.00026.0000.0000.0000.000163024.2030.0000.0000.000; > > > > > 0.0000.0001.0000.0000.0000.00031.0000.0000.0000.00042.0000.0000.0000.00033.0000.0000.0000.000140203.7970.000; > > > > > 0.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00029.0000.0000.0000.000186282.2970.000; > > > > > 0.0000.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00017.0000.0000.0000.000171746.094; > > > > > 0.0001.0000.0000.0000.00017.0000.0000.0000.00034.0000.0000.0000.00015.0000.0000.0000.000145005.2030.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.00015.0000.0000.0000.00054.0000.0000.0000.00027.0000.0000.0000.000168633.203; > > > > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00027.0000.0000.0000.00020.0000.0000.0000.000186731.297; > > > > > 0.0001.0000.0000.0000.0001.0000.0000.0000.00061.0000.0000.0000.00028.0000.0000.0000.000154627.5000.0000.000; > > > > > 0.0001.0000.0000.0000.00010.0000.0000.0000.00044.0000.0000.0000.00022.0000.0000.0000.000154626.2970.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.0004.0000.0000.0000.00059.0000.0000.0000.00020.0000.0000.0000.000177918.500; > > > > > 0.0001.0000.0000.0000.0004.0000.0000.0000.00056.0000.0000.0000.00027.0000.0000.0000.000157687.7970.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.0008.0000.0000.0000.00058.0000.0000.0000.00032.0000.0000.0000.000173899.094; > > > > > 0.0000.0000.0001.0000.0000.0000.00021.0000.0000.0000.00020.0000.0000.0000.00018.0000.0000.0000.000175980.500; > > > > > 0.0001.0000.0000.0000.0000.0000.0000.0000.00059.0000.0000.0000.00028.0000.0000.0000.000162526.7030.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.0002.0000.0000.0000.00037.0000.0000.0000.00020.0000.0000.0000.000198622.797; > > > > > 0.0001.0000.0000.0000.0003.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000157633.9060.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00021.0000.0000.0000.00021.0000.0000.0000.000164236.297; > > > > > 0.0001.0000.0000.0000.00022.0000.0000.0000.00046.0000.0000.0000.00023.0000.0000.0000.000144559.7030.0000.000; > > > > > 0.0001.0000.0000.0000.0007.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000156151.5000.0000.000; > > > > > 0.0000.0000.0001.0000.0000.0000.00016.0000.0000.0000.00046.0000.0000.0000.00027.0000.0000.0000.000154306.406; > > > > > 0.0000.0000.0001.0000.0000.0000.0000.0000.0000.0000.00019.0000.0000.0000.00020.0000.0000.0000.000188334.203; > > > > > 0.0001.0000.0000.0000.00020.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000134977.4060.0000.000; > > > > -------------------------------- > > > > ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5 > > > > -------------------------------- > > > > Possible problem with experimental design: > > > > Check for duplicate entries and/or lack of range of > > > > continuous variables within a class. > > > > If you seek help with this problem, make sure to send: > > > > 1. Your command line: > > > > mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C > > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat--C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > > > > 2. The FSGD file (if using one) > > > > 3. And the design matrix above > > > > Error in Analyze: command failed: mri_glmfit --y > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C > > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > > --C > > > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > > I also attach the error message. > > > > Could you tell me how I can fix this problem? > > > > I am looking forward to receiving your reply. > > > > Best regards, > > Seung-Gul > > > > *S**eung-Gul Kang, M.D., Ph.D. * > > Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center > > ?????. Dean, Department of Research Affairs; Gachon University > > College of Medicine > > ????????????.?Director, Incheon Suicide Prevention Center > > 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea > > > > ? > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 172, Issue 21 > ******************************************* > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
