[Freesurfer] complete list of structures for SubCortGray
Hi, >From https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats "SubCortGray - includes thalamus, caudate, hippocampus, amygdala, accumbens, ventral DC, substancia nigra (if there). This is a simple voxel count of structures identified as subcortical GM." Could you please let me know if "thalamus, caudate, hippocampus, amygdala, accumbens, ventral DC, substancia nigra (if there)" is the complete list of structures identified as subcortical GM or are there others? A simple voxel count of thalamus, caudate, hippocampus, amygdala, accumbens, ventral DC, substancia nigra (if there) does not seem to match the subcortgray value from aseg.stats. Versions 5.3, 6.0. Thanks. ___ 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 . 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.
Re: [Freesurfer] Error using LGI script despite making suggested chages to Matlab script.
Thanks for your help. Yes.
It looks like it is crashing during make_roi_paths.m
Any ideas? Thanks.
On Fri, 30 Sep 2016 06:32:06 -0700 Alan Francis
alandarkene...@gmail.com wrote
Hi Prasser:
Did you set the environment for MATLAB e.g.,
setenv MATLABPATH /Applications/MATLAB_version setenv PATH
${MATLABPATH}/bin:${PATH}
This is required for FS to source MATLAB.
best,
Alan
On Thu, Sep 29, 2016 at 6:46 PM, prasser pras...@zoho.com wrote:
Hi, Reposting. Thanks.
On Tue, 27 Sep 2016 16:53:21 -0700 prasserpras...@zoho.com wrote
Hi,
I'm looking to please get some help with -lgi.
I'm using matlab R2015b and FS5.3 with
recon-all -s subj_id -lgi
on os x 10.11.
Looking at the output, the first error occurs about here:
preparing pial mesh structure ...
...searching for mesh edges...done (206.94 sec).
... creating path file for vertex 1 / 65274
area file for outer ROIs saved at 1
In an assignment A(:) = B, the number of elements in A and B must be the same.
Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));
I have changed the script SearchProjectionOnPial.m as suggested on the
ReleaseNotes page.
Any help would be much appreciated.
Thanks.
___
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 . 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 . 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.
--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan N. Francis PhD
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.edu
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
___
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 . 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 . 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.
Re: [Freesurfer] Repost: Error using LGI script despite making suggested chages to Matlab script.
Hi, Reposting. Thanks. On Tue, 27 Sep 2016 16:53:21 -0700 prasserpras...@zoho.com wrote Hi, I'm looking to please get some help with -lgi. I'm using matlab R2015b and FS5.3 with recon-all -s subj_id -lgi on os x 10.11. Looking at the output, the first error occurs about here: preparing pial mesh structure ... ...searching for mesh edges...done (206.94 sec). ... creating path file for vertex 1 / 65274 area file for outer ROIs saved at 1 In an assignment A(:) = B, the number of elements in A and B must be the same. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); I have changed the script SearchProjectionOnPial.m as suggested on the ReleaseNotes page. Any help would be much appreciated. Thanks. ___ 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 . 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 . 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] mgz file format
Hi, When using mri_convert to create 001.mgz from dicom that have *not* been anonymized does any patient, institution, study description etc information get transferred into the 001.mgz? Thanks. ___ 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 . 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] Error using LGI script despite making suggested chages to Matlab script.
Hi, I'm looking to please get some help with -lgi. I'm using matlab R2015b and FS5.3 with recon-all -s subj_id -lgi on os x 10.11. Looking at the output, the first error occurs about here: preparing pial mesh structure ... ...searching for mesh edges...done (206.94 sec). ... creating path file for vertex 1 / 65274 area file for outer ROIs saved at 1 In an assignment A(:) = B, the number of elements in A and B must be the same. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); I have changed the script SearchProjectionOnPial.m as suggested on the ReleaseNotes page. Any help would be much appreciated. Thanks. ___ 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 . 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] coordinates to values
Hi, Could you please let me know the command that takes say, ras coordinates (or a list of them) and a .mgz as input, and outputs the corresponding voxel values from the .mgz? Thanks. ___ 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 . 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] FS 5.3 and OS X 10.11
Hi, On the download page it mentions that Freesurfer v5.3 is not compatible with OS X 10.11 because of an implementation of SIP. As a test, I have run a few subjects with v5.3 under OS X 10.11.3 with SIP enabled but was unable to see any problems, with all test subjects completing without error. I was wondering what I should be looking for (i.e. in the .log etc?) that would indicate that v5.3 is not compatible with OS X 10.11.3. Thanks. ___ 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 . 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] mean rate of change of thickness on fsaverage
Hi, I was hoping to get confirmation on the set of command below to display the mean rate of change of thickness on fsaverage from a group of subjects in a longitudinal study. Please let me know if I'm missing anything? Thanks, P mris_preproc --fsgd group.fsgd \ --cache-in long.thickness-rate.fwhm15.fsaverage \ --target fsaverage --hemi lh \ --out lh.group.long.thickness-rate.fwhm15.fsaverage.mgh followed by mri_concat --i lh.group.long.thickness-rate.fwhm15.fsaverage.mgh --mean \ --o lh.mean.group.long.thickness-rate.fwhm15.fsaverage.mgh then display this overlay with freeview -f ../fsaverage/surf/lh.pial:overlay=lh.mean.group.long.thickness-rate.fwhm15.fsaverage.mgh ___ 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 . 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] cross and long in qdec
Hi, If I have a set of subjects from a study collected at time 0 (T0) and a subset of these subjects that also have data collected at time 1 (T1), can I run qdec on the T0 subject's with no T1 together with the longs of the subject's at T0 that have a T1? Thanks, P ___ 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 . 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] nu_correct flag for memprage
Hi, For memprage data collected on a 3T scanner could you please let me know what nu_correct flag should be used for recon-all? Should we use -nuintensitycor-3T? Thanks, P ___ 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 . 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] control points from cross transferred to long
Hi, On this page https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits it mentions it is recommended to check if all CPs are accurately placed in the long. I was wondering what is the best way to do this? I know I can type in the RAS coordinates from the control.dat file and check each one this way, but this seems a little tedious and prone to errors especially as I can't paste into tkmedit. Also, is there a command that can get the intensity from brainmask.mgz from a given RAS coordinate? Thanks P ___ 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 . 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] ThickAvg of specific structures
Hi, If I am only interested in the gm thickness (ThickAvg) of a specific structure/s (e.g. precentral) is it sufficient to only QC these specific structures/s or does the wm and pial surface need to be accurate across the entire hemisphere for the accurate determination of gm thickness of the specified structure/s? Thanks, P ___ 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 . 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.
Re: [Freesurfer] where to start recon-all after edits
Hi, If the surfaces are 'done' and we update/edit the the aseg.mgz with recon-all -surfsegedit and then run recon-all -autorecon2-cp -autorecon3 to update the .stats, this also creates new wm and pial surfaces that may be different to those used for -surfsegedit. Is that right? As another alternative, could we run say, recon-all -autorecon2-cp_ -autorecon3_ that have set DoWhiteSurfs = 0; set DoPialSurfs = 0; so that new surfaces are not created and avoid needing to recheck the wm/pial surfaces (as they were previously considered done) as well as being the same as those used for the -surfsegedit. Looking forward to a reply, thanks, P On Mon, 18 May 2015 16:27:31 -0700 prasser lt;pras...@zoho.comgt; wrote Hi, This is a repost, hope someone can please comment? Thanks. On Wed, 06 May 2015 00:07:17 -0700 prasser lt;pras...@zoho.comgt; wrote Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after -surfsegedit is that, new surfaces are created during -autorecon2-cp -autorecon3 so that aseg and the surfaces are always out of step with each other. Any suggestions on how I could test the validity of the method described here as an alternative: recon-all -surfsegedit then edit aseg if needed and then: recon-all -aparc2aseg -segstats -wmparc On Tue, 05 May 2015 07:09:48 -0700 Martin Reuter lt;mreu...@nmr.mgh.harvard.edugt; wrote Yes, if this is in the long, you also need to add the -long …. stuff Martin On Apr 28, 2015, at 12:46 AM, prasser lt;pras...@zoho.comgt; wrote: Thanks for your response, not sure if I've quite got it yet. So, after the surfaces are done and we update/edit the the aseg.mgz with say, recon-all -surfsegedit we need to re-run recon-all -autorecon2-cp -autorecon3 On Thu, 23 Apr 2015 06:45:00 -0700 Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can comment? On Wed, 22 Apr 2015, prasser wrote: gt; Repost.Thanks. gt; gt; gt; On Mon, 20 Apr 2015 16:35:29 -0700 lt;pras...@zoho.comgt; wrote gt; gt; Thank you again for your reply. gt; gt; For editing aseg.mgz, as mentioned in gt; gt; https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegme gt; ntations gt; gt; it does suggest using -autorecon2-noaseg, but from what I can see this does not gt; update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't gt; this command (as does -autorecon3) also re-create surfaces that would need to be gt; re-checked and re-edited if needed? gt; gt; Also, I think FS5.1 does not have the -autorecon2-noaseg flag. gt; gt; As an alternative, with completed wm/pial boundaries could we run gt; gt; recon-all -surfsegedit, gt; gt; then we would edit aseg as needed and then: gt; gt; recon-all -aparc2aseg -segstats -wmparc gt; gt; This will not change any surfaces but would update aseg.stats gt; aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc gt; gt; P gt; gt; gt; On Mon, 20 Apr 2015 13:42:49 -0700 Martin gt; Reuterlt;mreu...@nmr.mgh.harvard.edugt; wrote gt; Hi gt; gt; so take a look at gt; https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData gt; where the entry points are described ( for brainmask and finalsurfs gt; -autorecon-pial should be OK, for aseg it says to use gt; gt; -autorecon2-noaseg ) gt; Also this page gt; https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags gt; has details on the steps. gt; gt; Best, Martin gt; gt; gt; gt; On 04/20/2015 03:21 PM, Martin Reuter wrote: gt; gt; usually edits to surfaces should not be required in the long. The gt; surfaces there get initialized from the base, so you need to make gt; sure the base surface is as accurate as possible. Several edits also gt; get transferred automatically from the cross sectional runs. See gt; this gt; http://freesurfer.net/fswiki/LongitudinalEdits gt; for a description of the different edits, and where they should be gt; done. gt; gt; About where to restart after making the edits, everything should be gt; done the same way as in the regular (cross sectional) processing. gt; So you specifically ask about: gt; - brainmask edits gt; - brainfinalsurf edits gt; - and manual aseg edits. gt; gt; I just looked at the description of those regular edits gt; http://freesurfer.net/fswiki/Edits gt; but sadly there it does not say where to start re-run either. I'll gt; try to find out and update that soon. gt; gt; I hope someone with editing experience can chime in and tell us. (I gt; changed the subject, so that it get's read). gt; gt; Cheers, Martin gt; gt; On 04/20/2015 09:44 AM, Bruce Fischl wrote: gt; gt; cheers gt; Bruce gt; gt; gt; On Mon, 20 Apr 2015, prasser wrote: gt; gt; Dear All, gt; I wanted to check that corrections to a Long pial gt
Re: [Freesurfer] where to start recon-all after edits
Hi, This is a repost, hope someone can please comment? Thanks. On Wed, 06 May 2015 00:07:17 -0700 prasser lt;pras...@zoho.comgt; wrote Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after -surfsegedit is that, new surfaces are created during -autorecon2-cp -autorecon3 so that aseg and the surfaces are always out of step with each other. Any suggestions on how I could test the validity of the method described here as an alternative: recon-all -surfsegedit then edit aseg if needed and then: recon-all -aparc2aseg -segstats -wmparc On Tue, 05 May 2015 07:09:48 -0700 Martin Reuter lt;mreu...@nmr.mgh.harvard.edugt; wrote Yes, if this is in the long, you also need to add the -long …. stuff Martin On Apr 28, 2015, at 12:46 AM, prasser lt;pras...@zoho.comgt; wrote: Thanks for your response, not sure if I've quite got it yet. So, after the surfaces are done and we update/edit the the aseg.mgz with say, recon-all -surfsegedit we need to re-run recon-all -autorecon2-cp -autorecon3 On Thu, 23 Apr 2015 06:45:00 -0700 Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can comment? On Wed, 22 Apr 2015, prasser wrote: gt; Repost.Thanks. gt; gt; gt; On Mon, 20 Apr 2015 16:35:29 -0700 lt;pras...@zoho.comgt; wrote gt; gt; Thank you again for your reply. gt; gt; For editing aseg.mgz, as mentioned in gt; gt; https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegme gt; ntations gt; gt; it does suggest using -autorecon2-noaseg, but from what I can see this does not gt; update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't gt; this command (as does -autorecon3) also re-create surfaces that would need to be gt; re-checked and re-edited if needed? gt; gt; Also, I think FS5.1 does not have the -autorecon2-noaseg flag. gt; gt; As an alternative, with completed wm/pial boundaries could we run gt; gt; recon-all -surfsegedit, gt; gt; then we would edit aseg as needed and then: gt; gt; recon-all -aparc2aseg -segstats -wmparc gt; gt; This will not change any surfaces but would update aseg.stats gt; aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc gt; gt; P gt; gt; gt; On Mon, 20 Apr 2015 13:42:49 -0700 Martin gt; Reuterlt;mreu...@nmr.mgh.harvard.edugt; wrote gt; Hi gt; gt; so take a look at gt; https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData gt; where the entry points are described ( for brainmask and finalsurfs gt; -autorecon-pial should be OK, for aseg it says to use gt; gt; -autorecon2-noaseg ) gt; Also this page gt; https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags gt; has details on the steps. gt; gt; Best, Martin gt; gt; gt; gt; On 04/20/2015 03:21 PM, Martin Reuter wrote: gt; gt; usually edits to surfaces should not be required in the long. The gt; surfaces there get initialized from the base, so you need to make gt; sure the base surface is as accurate as possible. Several edits also gt; get transferred automatically from the cross sectional runs. See gt; this gt; http://freesurfer.net/fswiki/LongitudinalEdits gt; for a description of the different edits, and where they should be gt; done. gt; gt; About where to restart after making the edits, everything should be gt; done the same way as in the regular (cross sectional) processing. gt; So you specifically ask about: gt; - brainmask edits gt; - brainfinalsurf edits gt; - and manual aseg edits. gt; gt; I just looked at the description of those regular edits gt; http://freesurfer.net/fswiki/Edits gt; but sadly there it does not say where to start re-run either. I'll gt; try to find out and update that soon. gt; gt; I hope someone with editing experience can chime in and tell us. (I gt; changed the subject, so that it get's read). gt; gt; Cheers, Martin gt; gt; On 04/20/2015 09:44 AM, Bruce Fischl wrote: gt; gt; cheers gt; Bruce gt; gt; gt; On Mon, 20 Apr 2015, prasser wrote: gt; gt; Dear All, gt; I wanted to check that corrections to a Long pial gt; surface through edits gt; to brainmask.mgz and brain.finalsurfs.manedit.mgz gt; are followed by the gt; command: gt; recon-all -long tpN1 templateID -autorecon2-pial gt; -autorecom3 gt; gt; Is this correct? gt; gt; Also, after editing the Long aseg.mgz to correct gt; the volume of structures gt; what command should be run to have these edits gt; update the dependent files? gt; gt; Thanks, gt; gt; P gt; gt; gt; gt; gt; gt; ___ Freesurfer mailing list freesur...@nmr.mgh.h gt; arvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer gt; gt; gt; -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neurosci gt; ence Dept. of Radiology
Re: [Freesurfer] where to start recon-all after edits
Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after -surfsegedit is that, new surfaces are created during -autorecon2-cp -autorecon3 so that aseg and the surfaces are always out of step with each other. Any suggestions on how I could test the validity of the method described here as an alternative: recon-all -surfsegedit then edit aseg if needed and then: recon-all -aparc2aseg -segstats -wmparc On Tue, 05 May 2015 07:09:48 -0700 Martin Reuter lt;mreu...@nmr.mgh.harvard.edugt; wrote Yes, if this is in the long, you also need to add the -long …. stuff Martin On Apr 28, 2015, at 12:46 AM, prasser lt;pras...@zoho.comgt; wrote: Thanks for your response, not sure if I've quite got it yet. So, after the surfaces are done and we update/edit the the aseg.mgz with say, recon-all -surfsegedit we need to re-run recon-all -autorecon2-cp -autorecon3 On Thu, 23 Apr 2015 06:45:00 -0700 Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can comment? On Wed, 22 Apr 2015, prasser wrote: gt; Repost.Thanks. gt; gt; gt; On Mon, 20 Apr 2015 16:35:29 -0700 lt;pras...@zoho.comgt; wrote gt; gt; Thank you again for your reply. gt; gt; For editing aseg.mgz, as mentioned in gt; gt; https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegme gt; ntations gt; gt; it does suggest using -autorecon2-noaseg, but from what I can see this does not gt; update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't gt; this command (as does -autorecon3) also re-create surfaces that would need to be gt; re-checked and re-edited if needed? gt; gt; Also, I think FS5.1 does not have the -autorecon2-noaseg flag. gt; gt; As an alternative, with completed wm/pial boundaries could we run gt; gt; recon-all -surfsegedit, gt; gt; then we would edit aseg as needed and then: gt; gt; recon-all -aparc2aseg -segstats -wmparc gt; gt; This will not change any surfaces but would update aseg.stats gt; aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc gt; gt; P gt; gt; gt; On Mon, 20 Apr 2015 13:42:49 -0700 Martin gt; Reuterlt;mreu...@nmr.mgh.harvard.edugt; wrote gt; Hi gt; gt; so take a look at gt; https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData gt; where the entry points are described ( for brainmask and finalsurfs gt; -autorecon-pial should be OK, for aseg it says to use gt; gt; -autorecon2-noaseg ) gt; Also this page gt; https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags gt; has details on the steps. gt; gt; Best, Martin gt; gt; gt; gt; On 04/20/2015 03:21 PM, Martin Reuter wrote: gt; gt; usually edits to surfaces should not be required in the long. The gt; surfaces there get initialized from the base, so you need to make gt; sure the base surface is as accurate as possible. Several edits also gt; get transferred automatically from the cross sectional runs. See gt; this gt; http://freesurfer.net/fswiki/LongitudinalEdits gt; for a description of the different edits, and where they should be gt; done. gt; gt; About where to restart after making the edits, everything should be gt; done the same way as in the regular (cross sectional) processing. gt; So you specifically ask about: gt; - brainmask edits gt; - brainfinalsurf edits gt; - and manual aseg edits. gt; gt; I just looked at the description of those regular edits gt; http://freesurfer.net/fswiki/Edits gt; but sadly there it does not say where to start re-run either. I'll gt; try to find out and update that soon. gt; gt; I hope someone with editing experience can chime in and tell us. (I gt; changed the subject, so that it get's read). gt; gt; Cheers, Martin gt; gt; On 04/20/2015 09:44 AM, Bruce Fischl wrote: gt; gt; cheers gt; Bruce gt; gt; gt; On Mon, 20 Apr 2015, prasser wrote: gt; gt; Dear All, gt; I wanted to check that corrections to a Long pial gt; surface through edits gt; to brainmask.mgz and brain.finalsurfs.manedit.mgz gt; are followed by the gt; command: gt; recon-all -long tpN1 templateID -autorecon2-pial gt; -autorecom3 gt; gt; Is this correct? gt; gt; Also, after editing the Long aseg.mgz to correct gt; the volume of structures gt; what command should be run to have these edits gt; update the dependent files? gt; gt; Thanks, gt; gt; P gt; gt; gt; gt; gt; gt; ___ Freesurfer mailing list freesur...@nmr.mgh.h gt; arvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer gt; gt; gt; -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neurosci gt; ence Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusett gt; s General Hospital Research Affiliate Computer Science and Artificial Intelligence
Re: [Freesurfer] where to start recon-all after edits
Repost.Thanks. On Mon, 20 Apr 2015 16:35:29 -0700 lt;pras...@zoho.comgt; wrote Thank you again for your reply. For editing aseg.mgz, as mentioned in https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations it does suggest using -autorecon2-noaseg, but from what I can see this does not update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't this command (as does -autorecon3) also re-create surfaces that would need to be re-checked and re-edited if needed? Also, I think FS5.1 does not have the -autorecon2-noaseg flag. As an alternative, with completed wm/pial boundaries could we run recon-all -surfsegedit, then we would edit aseg as needed and then: recon-all -aparc2aseg -segstats -wmparc This will not change any surfaces but would update aseg.stats aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc P On Mon, 20 Apr 2015 13:42:49 -0700 Martin Reuterlt;mreu...@nmr.mgh.harvard.edugt; wrote Hi so take a look at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData where the entry points are described ( for brainmask and finalsurfs -autorecon-pial should be OK, for aseg it says to use -autorecon2-noaseg ) Also this page https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags has details on the steps. Best, Martin On 04/20/2015 03:21 PM, Martin Reuter wrote: blockquote cite=mid:lt;agt;553551cf.30...@nmr.mgh.harvard.edu type=cite gt;= hi= p, usually edits to surfaces should not be required in the long. The surfaces there get initialized from the base, so you need to make sure the base surface is as accurate as possible. Several edits also get transferred automatically from the cross sectional runs. See this http://freesurfer.net/fswiki/LongitudinalEdits for a description of the different edits, and where they should be done. About where to restart after making the edits, everything should be done the same way as in the regular (cross sectional) processing. So you specifically ask about: - brainmask edits - brainfinalsurf edits - and manual aseg edits. I just looked at the description of those regular edits http://freesurfer.net/fswiki/Edits but sadly there it does not say where to start re-run either. I'll try to find out and update that soon. I hope someone with editing experience can chime in and tell us. (I changed the subject, so that it get's read). Cheers, Martin On 04/20/2015 09:44 AM, Bruce Fischl wrote: blockquote cite=mid:alpilt;agt;ne.lrh.2.11.1504200944020.9...@gate.nmr.mgh.harvard.edu type=cite gt;i'll= leave= the= first= question= for= martin= but= it= looks= right= to= me= (except= typo= in= what= should= be= -autorecon3).= second= one= i= think= you= want= rerun= mri_segstats= and= mris_anatomical_stats= commands,= which= done= by= autorecon3= cheers Bruce On Mon, 20 Apr 2015, prasser wrote: Dear All, I wanted to check that corrections to a Long pial surface through edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command: recon-all -long tpN1 templateID -autorecon2-pial -autorecom3 Is this correct? Also, after editing the Long aseg.mgz to correct the volume of structures what command should be run to have these edits update the dependent files? Thanks, P ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https
Re: [Freesurfer] Edits to longitudinal pial surface and aseg
Repost.Thanks. On Mon, 20 Apr 2015 16:21:38 -0700 lt;pras...@zoho.comgt; wrote Thank you for your reply. Yes, I'm finding that it is only small edits that are required in the Long for the case of pial surface errors. It is usually in areas where no editing was required in the cross and base, but the pial surface in the Long extends to include dura or cerebellum. I was hoping just to edit the Long brainmask.mgz and brain.finalsurfs.manedit.mgz and re-run with the command recon-all -long tpN1 templateID -autorecon2-pial -autorecon3 and then re-check the surfaces. The alternative as I see it would be 1. Identify the corresponding locations in the Base (even though it is not a problem in the Base) 2. edit, re-run and re-check the Base 3. delete, create and check all new Longs This second option would take a considerable amount of time and may not solve the problem in one iteration. I'm guessing the concerns with the first method are introducing bias any other concerns with editing the Long? P On Mon, 20 Apr 2015 12:21:51 -0700 Martin Reuter lt;mreu...@nmr.mgh.harvard.edugt; wrote Hi P, usually edits to surfaces should not be required in the long. The surfaces there get initialized from the base, so you need to make sure the base surface is as accurate as possible. Several edits also get transferred automatically from the cross sectional runs. See this http://freesurfer.net/fswiki/LongitudinalEdits for a description of the different edits, and where they should be done. About where to restart after making the edits, everything should be done the same way as in the regular (cross sectional) processing. So you specifically ask about: - brainmask edits - brainfinalsurf edits - and manual aseg edits. I just looked at the description of those regular edits http://freesurfer.net/fswiki/Edits but sadly there it does not say where to start re-run either. I'll try to find out and update that soon. I hope someone with editing experience can chime in and tell us. (I changed the subject, so that it get's read). Cheers, Martin On 04/20/2015 09:44 AM, Bruce Fischl wrote: blockquote cite=mid:alpilt;agt;ne.lrh.2.11.1504200944020.9...@gate.nmr.mgh.harvard.edu type=cite gt;i'll= leave= the= first= question= for= martin= but= it= looks= right= to= me= (except= typo= in= what= should= be= -autorecon3).= second= one= i= think= you= want= rerun= mri_segstats= and= mris_anatomical_stats= commands,= which= done= by= autorecon3= cheers Bruce On Mon, 20 Apr 2015, prasser wrote: Dear All, I wanted to check that corrections to a Long pial surface through edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command: recon-all -long tpN1 templateID -autorecon2-pial -autorecom3 Is this correct? Also, after editing the Long aseg.mgz to correct the volume of structures what command should be run to have these edits update the dependent files? Thanks, P ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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 . 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 . 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.
Re: [Freesurfer] Edits to longitudinal pial surface and aseg
Thank you for your reply. Yes, I'm finding that it is only small edits that are required in the Long for the case of pial surface errors. It is usually in areas where no editing was required in the cross and base, but the pial surface in the Long extends to include dura or cerebellum. I was hoping just to edit the Long brainmask.mgz and brain.finalsurfs.manedit.mgz and re-run with the command recon-all -long tpN1 templateID -autorecon2-pial -autorecon3 and then re-check the surfaces. The alternative as I see it would be 1. Identify the corresponding locations in the Base (even though it is not a problem in the Base) 2. edit, re-run and re-check the Base 3. delete, create and check all new Longs This second option would take a considerable amount of time and may not solve the problem in one iteration. I'm guessing the concerns with the first method are introducing bias any other concerns with editing the Long? P On Mon, 20 Apr 2015 12:21:51 -0700 Martin Reuter lt;mreu...@nmr.mgh.harvard.edugt; wrote Hi P, usually edits to surfaces should not be required in the long. The surfaces there get initialized from the base, so you need to make sure the base surface is as accurate as possible. Several edits also get transferred automatically from the cross sectional runs. See this http://freesurfer.net/fswiki/LongitudinalEdits for a description of the different edits, and where they should be done. About where to restart after making the edits, everything should be done the same way as in the regular (cross sectional) processing. So you specifically ask about: - brainmask edits - brainfinalsurf edits - and manual aseg edits. I just looked at the description of those regular edits http://freesurfer.net/fswiki/Edits but sadly there it does not say where to start re-run either. I'll try to find out and update that soon. I hope someone with editing experience can chime in and tell us. (I changed the subject, so that it get's read). Cheers, Martin On 04/20/2015 09:44 AM, Bruce Fischl wrote: ne.lrh.2.11.1504200944020.9...@gate.nmr.mgh.harvard.edu type=citegt;I'll leave the first question for Martin but it looks right to me (except for the typo in what should be -autorecon3). For the second one I think you want to rerun the mri_segstats and mris_anatomical_stats commands, which should be done by autorecon3 cheers Bruce On Mon, 20 Apr 2015, prasser wrote: Dear All, I wanted to check that corrections to a Long pial surface through edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command: recon-all -long tpN1 templateID -autorecon2-pial -autorecom3 Is this correct? Also, after editing the Long aseg.mgz to correct the volume of structures what command should be run to have these edits update the dependent files? Thanks, P ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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 . 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 . 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.
Re: [Freesurfer] where to start recon-all after edits
Thank you again for your reply. For editing aseg.mgz, as mentioned in https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations it does suggest using -autorecon2-noaseg, but from what I can see this does not update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't this command (as does -autorecon3) also re-create surfaces that would need to be re-checked and re-edited if needed? Also, I think FS5.1 does not have the -autorecon2-noaseg flag. As an alternative, with completed wm/pial boundaries could we run recon-all -surfsegedit, then we would edit aseg as needed and then: recon-all -aparc2aseg -segstats -wmparc This will not change any surfaces but would update aseg.stats aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc P On Mon, 20 Apr 2015 13:42:49 -0700 Martin Reuterlt;mreu...@nmr.mgh.harvard.edugt; wrote Hi so take a look at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData where the entry points are described ( for brainmask and finalsurfs -autorecon-pial should be OK, for aseg it says to use -autorecon2-noaseg ) Also this page https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags has details on the steps. Best, Martin On 04/20/2015 03:21 PM, Martin Reuter wrote: 553551cf.30...@nmr.mgh.harvard.edu type=citegt; Hi P, usually edits to surfaces should not be required in the long. The surfaces there get initialized from the base, so you need to make sure the base surface is as accurate as possible. Several edits also get transferred automatically from the cross sectional runs. See this http://freesurfer.net/fswiki/LongitudinalEdits for a description of the different edits, and where they should be done. About where to restart after making the edits, everything should be done the same way as in the regular (cross sectional) processing. So you specifically ask about: - brainmask edits - brainfinalsurf edits - and manual aseg edits. I just looked at the description of those regular edits http://freesurfer.net/fswiki/Edits but sadly there it does not say where to start re-run either. I'll try to find out and update that soon. I hope someone with editing experience can chime in and tell us. (I changed the subject, so that it get's read). Cheers, Martin On 04/20/2015 09:44 AM, Bruce Fischl wrote: ne.lrh.2.11.1504200944020.9...@gate.nmr.mgh.harvard.edu type=citegt;I'll leave the first question for Martin but it looks right to me (except for the typo in what should be -autorecon3). For the second one I think you want to rerun the mri_segstats and mris_anatomical_stats commands, which should be done by autorecon3 cheers Bruce On Mon, 20 Apr 2015, prasser wrote: Dear All, I wanted to check that corrections to a Long pial surface through edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command: recon-all -long tpN1 templateID -autorecon2-pial -autorecom3 Is this correct? Also, after editing the Long aseg.mgz to correct the volume of structures what command should be run to have these edits update the dependent files? Thanks, P ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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
[Freesurfer] Edits to longitudinal pial surface and aseg
Dear All, I wanted to check that corrections to a Long pial surface through edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command: recon-all -long tpN1 templateID -autorecon2-pial -autorecom3 Is this correct? Also, after editing the Long aseg.mgz to correct the volume of structures what command should be run to have these edits update the dependent files? Thanks, P ___ 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 . 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.
Re: [Freesurfer] sMRI using Freesurfer 5.1 followed by DTI using Freesufer 5.3
Say, following the set of commands given on the FsTutorial/Diffusion page (freesurfer.net/fswiki/FsTutorial/Diffusion) On Mon, 15 Sep 2014 05:26:01 -0700 Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote what kind of DTI analysis? On Sun, 14 Sep 2014, prasser wrote: gt; Hi, gt; gt; Could you please let me know if it's okay to use subjects analyzed using gt; Freesurfer 5.1 (os x 10.6) for DTI analysis using Freesurfer 5.3 (os x gt; 10.8)? gt; gt; Thanks. gt; gt; gt; gt; gt; ___ 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 . 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 . 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] sMRI using Freesurfer 5.1 followed by DTI using Freesufer 5.3
Hi, Could you please let me know if it's okay to use subjects analyzed using Freesurfer 5.1 (os x 10.6) for DTI analysis using Freesurfer 5.3 (os x 10.8)? Thanks. ___ 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 . 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] repost: transforming Base surfaces to Cross space for longitudinal data sets
Dear All, For longitudinal data sets, is there a way that the lh.pial surface from the Base can be transformed into the brainmask.mgz space of a Cross so that it can be viewed with tkmedit on the Cross brainmask.mgz? Thanks, Paul ___ 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 . 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] transforming Base surfaces to Cross space
Dear All, For longitudinal data sets, is there a way that the lh.pial surface from the Base can be transformed into the brainmask.mgz space of a Cross so that it can be viewed with tkmedit on the Cross brainmask.mgz? Thanks, Paul ___ 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 . 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.
Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3
Other than orientation, (which could be deduced from visual inspection of fiducial markers or other) are there any other concerns with this approach?Paul On Tue, 29 Apr 2014 09:04:00 -0700 Douglas N Greve lt;gr...@nmr.mgh.harvard.edugt; wrote I don't know that it would be preferred or acceptable. You have just thrown away information about what is left and right, so you might have inadvertently flipped the brain. Unless your voxel size is 1mm, there will be some interpolation when conforming. I'm not that worried about the interpolation artifact that you see in tkmedit/freeview doug On 04/28/2014 11:53 PM, prasser wrote: gt; gt; Thanks. gt; gt; Using: gt; gt; mri_convert dicom output.nii -iid 0 -1 0 -ijd 0 0 -1 -ikd -1 0 0 gt; gt; gt; Seems to do the trick. gt; gt; I have attached a figure with the left image from mri_convert and the gt; right image using mri_convert and the flags listed above, both viewed gt; using tkmedit. gt; gt; gt; From a visual perspective I prefer the right hand image, and wonder if gt; this striping appearance in the left hand image is smoothed when gt; creating orig.mgz using the --conform flag? gt; gt; Would using: gt; gt; mri_convert dicom output.nii -iid 0 -1 0 -ijd 0 0 -1 -ikd -1 0 0 gt; gt; mri_convert output.nii orig.mgz --conform gt; gt; be preferred (or acceptable) in this case? gt; gt; Paul gt; gt; gt; On Mon, 28 Apr 2014 14:55:27 -0700 *Douglas N Greve gt; lt;gr...@nmr.mgh.harvard.edugt;* wrote gt; gt; gt; I don't think this is aproblem either. tkmedit/freeview will be gt; showing gt; it in the acquisition RAS space (not the image coordinate space). I gt; don't think there is anything wrong with the actual data. If the gt; volumes gt; from other packages do not show up this way in tkmedit/fv then it may gt; mean that they are throwing away this information. You can throw gt; it away gt; too when you run mri_convert, something like gt; gt; mri_convert dicom output.nii -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 gt; gt; see if that at least causes the funny images to go away. gt; gt; gt; On 04/27/2014 10:35 PM, prasser wrote: gt; gt; Thanks for your reply. gt; gt; gt; gt; Yes, I can upload the data. Is there a private area I can upload gt; to? gt; gt; gt; gt; Also, is there a flag that enables acquisition slice space info gt; to be gt; gt; used with tkmedit? gt; gt; gt; gt; Lastly, when converting to .nii with other packages and viewing gt; with gt; gt; tkmedit the acquisition slice space seems to be taken into account. gt; gt; gt; gt; Paul gt; gt; gt; gt; gt; gt; gt; gt; gt; gt; gt; gt; On Sun, 27 Apr 2014 17:33:02 -0700 *Bruce Fischl gt; gt; lt;fis...@nmr.mgh.harvard.edu gt; lt;mailto:fis...@nmr.mgh.harvard.edugt;gt;* wrote gt; gt; gt; gt; Hi Paul gt; gt; gt; gt; perhaps Ruopeng can comment, but I suspect this isn't a problem - gt; gt; it's gt; gt; just showing it to you in a standard anatomical space not the gt; gt; slice spaceit gt; gt; was acquired in. If you want to upload the dataset we can take a gt; gt; look and gt; gt; confirm gt; gt; gt; gt; cheers gt; gt; Bruce gt; gt; gt; gt; gt; gt; On Sun, 27 Apr 2014, prasser wrote: gt; gt; gt; gt; gt; Hi, gt; gt; gt; gt; gt; gt; I am still having some concerns using mri_convert on Skyra gt; gt; volumes that I'm gt; gt; gt; hoping can please be addressed. gt; gt; gt; gt; gt; gt; On this occasion I have used mri_convert to convert a single gt; gt; dicom file to gt; gt; gt; nifti from a volume collected on a siemens Skyra scanner using gt; gt; Freesurfer5.3 gt; gt; gt; on CentOS5.7. gt; gt; gt; gt; gt; gt; When viewing this nifti image using tkmedit it appears 'cut-up' gt; gt; over many gt; gt; gt; sagittal slices (please see attached) rather than the whole gt; gt; image appearing gt; gt; gt; on one plane. gt; gt; gt; gt; gt; gt; Not sure if this is an issue with tkmedit or mri_convert? gt; gt; gt; gt; gt; gt; This problem persists if i convert the entire volume, with this gt; gt; 'cutting' gt; gt; gt; appearing as vertical lines in the image. gt; gt; gt; gt; gt; gt; This is also the case when using the new mri_convert patch for gt; gt; OS X. gt; gt; gt; gt; gt; gt; Lastly, I can upload a dicom file if needed. gt; gt; gt; gt; gt; gt; Thanks, gt; gt; gt; Paul gt; gt; gt; gt; gt; gt; gt; gt; gt; gt; gt; ___ gt; gt; Freesurfer mailing list gt; gt; Freesurfer@nmr.mgh.harvard.edu gt; lt;mailto:Freesurfer@nmr.mgh.harvard.edugt; gt; gt; lt;mailto:Freesurfer@nmr.mgh.harvard.edugt; gt; gt; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer gt; gt; gt; gt; gt; gt; The information in this e-mail is intended only for the person to gt; gt; whom it is gt; gt; addressed. If you believe this e-mail was sent to you in error and gt; gt; the e-mail gt; gt; contains patient information, please contact the Partners gt
[Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3
Hi, I am still having some concerns using mri_convert on Skyra volumes that I'm hoping can please be addressed. On this occasion I have used mri_convert to convert a single dicom file to nifti from a volume collected on a siemens Skyra scanner using Freesurfer5.3 on CentOS5.7. When viewing this nifti image using tkmedit it appears 'cut-up' over many sagittal slices (please see attached) rather than the whole image appearing on one plane. Not sure if this is an issue with tkmedit or mri_convert? This problem persists if i convert the entire volume, with this 'cutting' appearing as vertical lines in the image. This is also the case when using the new mri_convert patch for OS X. Lastly, I can upload a dicom file if needed. Thanks, Paul Screenshot_crop.pdf Description: Binary data ___ 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 . 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.
Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3
Thanks for your reply. Yes, I can upload the data. Is there a private area I can upload to? Also, is there a flag that enables acquisition slice space info to be used with tkmedit? Lastly, when converting to .nii with other packages and viewing with tkmedit the acquisition slice space seems to be taken into account. Paul On Sun, 27 Apr 2014 17:33:02 -0700 Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote Hi Paul perhaps Ruopeng can comment, but I suspect this isn't a problem - it's just showing it to you in a standard anatomical space not the slice spaceit was acquired in. If you want to upload the dataset we can take a look and confirm cheers Bruce On Sun, 27 Apr 2014, prasser wrote: gt; Hi, gt; gt; I am still having some concerns using mri_convert on Skyra volumes that I'm gt; hoping can please be addressed. gt; gt; On this occasion I have used mri_convert to convert a single dicom file to gt; nifti from a volume collected on a siemens Skyra scanner using Freesurfer5.3 gt; on CentOS5.7. gt; gt; When viewing this nifti image using tkmedit it appears 'cut-up' over many gt; sagittal slices (please see attached) rather than the whole image appearing gt; on one plane. gt; gt; Not sure if this is an issue with tkmedit or mri_convert? gt; gt; This problem persists if i convert the entire volume, with this 'cutting' gt; appearing as vertical lines in the image. gt; gt; This is also the case when using the new mri_convert patch for OS X. gt; gt; Lastly, I can upload a dicom file if needed. gt; gt; Thanks, gt; Paul gt; gt; gt; ___ 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 . 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 . 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] mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3
Hi, I am still having some concerns using mri_convert on Skyra volumes that I'm hoping can please be addressed. On this occasion I have used mri_convert to convert a single dicom file to nifti from a volume collected on a siemens Skyra scanner using Freesurfer5.3 on CentOS5.7. When viewing this nifti image using tkmedit it appears 'cut-up' over many sagittal slices (please see attached) rather than the whole image appearing on one plane. Not sure if this is an issue with tkmedit or mri_convert? This problem persists if i convert the entire volume, with this 'cutting' appearing as vertical lines in the image. This is also the case when using the new mri_convert patch for OS X. Lastly, I can upload a dicom file if needed. Thanks, Paul Screenshot_crop.pdf Description: Binary data ___ 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 . 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.
Re: [Freesurfer] mri_convert Siemens .IMA error
Thanks, but the orientation shift appears as a skew. Also, we don't have any fiducial markers for this group of scans so it would be a little tricky to confirm the correct application of -out_orientation. I would rather let mri_convert handle this from the .IMAs. Is there any additional information I can provide from from the .IMA header etc that could shed some light on why mri_convert is behaving in this way? Thanks, Paul On Wed, 04 Dec 2013 22:11:27 -0800 Mark Plantz lt;markplantz2...@u.northwestern.edugt; wrote Not sure if this helps, but you can alter the output orientation using the flag --out_orientation followed by LIA (for example). Maybe the input file needs to be in a specific orientation before it can be converted properly. On Wed, Dec 4, 2013 at 9:56 PM, prasser lt;pras...@zoho.comgt; wrote: Hi, I'm currently having problems converting .IMA files collected from a Siemens Skyra to .mgz format using mri_convert from Freesurfer5.3 on os x. Using: mri_convert -it siemens -ot mgz 1.IMA test.mgz I get the error message: does not contain a Siemens ASCII header has this file been anonymised? ERROR: cannot unpack mosiacs without ASCII header The .IMA files have been taken straight from the scanner console. If I try: mri_convert -it dicom -ot mgz 1.IMA test.mgz this creates the .mgz, however there is an orientation shift and a vertical stripe artefact appears in the sagittal view (please see attached) when compared to the original .IMA. Any suggestions on how to convert the Siemens .IMA files correctly? Thanks, Paul ___ 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 . 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 . 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 . 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] mri_convert Siemens .IMA error
Hi, I'm currently having problems converting .IMA files collected from a Siemens Skyra to .mgz format using mri_convert from Freesurfer5.3 on os x. Using: mri_convert -it siemens -ot mgz 1.IMA test.mgz I get the error message: does not contain a Siemens ASCII header has this file been anonymised? ERROR: cannot unpack mosiacs without ASCII header The .IMA files have been taken straight from the scanner console. If I try: mri_convert -it dicom -ot mgz 1.IMA test.mgz this creates the .mgz, however there is an orientation shift and a vertical stripe artefact appears in the sagittal view (please see attached) when compared to the original .IMA. Any suggestions on how to convert the Siemens .IMA files correctly? Thanks, Paul ___ 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 . 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.
Re: [Freesurfer] Fwd: white matter and pial surface don't track sulcus
The flag -autorecon2-noaseg seems to no longer be used in version 5.1. i.e. ERROR: Flag -autorecon2-noaseg unrecognized. For edits made to aseg.mgz, could you please let me know what recon-all flags are recommended for version 5.1 for the case described in the email below? Thanks. On Sun, 16 Sep 2012 16:07:20 -0700 Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote Yes On Sep 16, 2012, at 6:13 PM, Darren Gitelman lt;d-gitel...@northwestern.edugt; wrote: Yes. That's it. I tried editing the wm.mgz earlier and deleting all voxels labels as ventricle (250) but that didn't solve the problem. Do I edit the aseg.mgz file and just label it as none in this region? Would I use the command tkmedit lt;subjidgt; brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt When done do I run recon-all -autorecon2-noaseg -autorecon3? Thanks, Darren On Sun, Sep 16, 2012 at 4:38 PM, Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote: Check the aseg and see if it was labeled ventricle (and make sure it really isn't). You may need to edit the aseg On Sep 16, 2012, at 5:19 PM, Darren Gitelman lt;d-gitel...@northwestern.edugt; wrote: Hi I have run into an issue that I'm not sure how to correct. What happens is that in some subjects the surfaces don't seem to properly track sulci coming off the medial part of temporo-occipital cortex. Please see green arrows on the attached image. In fact the tutorial on topological defects shows an image with a similar issue, but fixing it is not discussed. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?action=AttachFileamp;do=getamp;target=TopoafterBM.jpg I have checked and these are sulci and not the occipital extent of the lateral ventricle. Perhaps it is not a problem, or if it is then how to approach fixing it? Thank you, Darren -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 lt;3809-error.pnggt; ___ 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 . 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. -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ 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 . 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 . 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.
Re: [Freesurfer] mri_cnr
Hi, I was wondering if there is any documentation on mri_cnr, particularly how the noise is calculated. Thank you, Paul gt; gt; thanks Dr. B.that helped a lot gt; gt; - Original Message - gt; From: Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; gt; To: Kushal Kapse lt;kka...@mail.med.upenn.edugt; gt; Cc: freesurfer lt;freesurfer@nmr.mgh.harvard.edugt; gt; Sent: Monday, June 18, 2012 2:27:29 PM gt; Subject: Re: [Freesurfer] mri_cnr gt; gt; Hi KK gt; gt; this is something i wrote for myself, but you are welcome to try it out. gt; YOu don't need to give it the slope stuff, that is optional. The vol gt; command line parms are the volumes that you want to assess CNR in. For gt; example: gt; gt; mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz gt; processing MRI volume /homes/4/fischl/local_subjects/bruce/mri/norm.mgz... gt; white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2 gt; gray/white CNR = 2.241, gray/csf CNR = 1.026 gt; lh CNR = 1.633 gt; white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4 gt; gray/white CNR = 2.205, gray/csf CNR = 0.937 gt; rh CNR = 1.571 gt; total CNR = 1.602 gt; gt; gt; On Mon, gt; 18 Jun 2012, Kushal Kapse wrote: gt; gt; gt; hi fellas, gt; gt; gt; gt; i am trying to run mri_cnr command in freesurfer to compute and see CNR for gray/white/csf the command gives following info as help: gt; gt; gt; gt; -bash-3.2$ mri_cnr gt; gt; usage: mri_cnr [options] lt;surf directorygt; lt;vol 1gt; lt;vol 2gt; ... gt; gt; -s lt;slope fnamegt; lt;dist ingt; lt;dist outgt; lt;step ingt; lt;step outgt; gt; gt; gt; gt; gt; gt; i understand that 'surf directory'= subjects 'surf' folder ; but i am not able to figure out what it means by vol1, vol2 and slope fname..it doesnt show any error but just doesnt do anything even if i mention the surf directory to this command. gt; gt; gt; gt; i checked on freesurfer mail archive, but no info since 2009 about any update on this command. gt; gt; gt; gt; may someone please give an info if anyone ever used this command gt; gt; gt; gt; gt; gt; thanks gt; gt; kk gt; gt; ___ gt; gt; Freesurfer mailing list gt; gt; Freesurfer@nmr.mgh.harvard.edu gt; gt; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer gt; gt; gt; gt; gt; gt; gt; ___ gt; Freesurfer mailing list gt; Freesurfer@nmr.mgh.harvard.edu gt; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer gt; gt; gt; The information in this e-mail is intended only for the person to whom it is gt; addressed. If you believe this e-mail was sent to you in error and the e-mail gt; contains patient information, please contact the Partners Compliance HelpLine at gt; http://www.partners.org/complianceline . If the e-mail was sent to you in error gt; but does not contain patient information, please contact the sender and properly gt; dispose of the e-mail. gt; gt; ___ gt; Freesurfer mailing list gt; Freesurfer@nmr.mgh.harvard.edu gt; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer gt; ___ 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 . 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.
