Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

crop a volume
by Yang Liu 04 Apr '11

04 Apr '11

Hi surfers, I have two volumes, one is 96*96*50*272, and the other is 84*96*50*272. I want to do motion correction between the two. But I have to make their spatial size to be identical. Is there a command in Freesurfer that can crop the size 96 to 84? Thanks. Yang

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Re: [Freesurfer] incorrect GM/WM surfaces
by Mayuresh K 03 Apr '11

03 Apr '11

Hi Dan and Bruce, Thanks for your getting back on the problem. My concern is more about the dura being incorrectly labeled - It appears to me that the grey-CSF boundary has been incorrectly labeled as the GM-WM boundary across the entire image. Any ideas what may have gone wrong? Thanks, Mayuresh On Sat, Apr 2, 2011 at 3:28 AM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: incorrect GM/WM surfaces (Daniel G Wakeman) > 2. problems with loading a pial surface (Iris Steinmann) > 3. Re: incorrect GM/WM surfaces (Bruce Fischl) > 4. Re: problems with loading a pial surface (Bruce Fischl) > 5. preproc-sess OSX bug fix getrunlist (Juli Dolzhenko) > 6. MRI analyst position (Keith Schneider) > 7. Distance between two points along cortical (caoaize) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Apr 2011 05:53:20 +0100 > From: Daniel G Wakeman <Daniel.Wakeman(a)mrc-cbu.cam.ac.uk> > Subject: Re: [Freesurfer] incorrect GM/WM surfaces > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <471C0967-FE19-409E-8174-31FBB56CDE1E(a)mrc-cbu.cam.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Hi Mayuresh, > > I assume you are talking about the area in the posterior midline, where the > pial surface seems to go 'squiggly'. You also seem to have a problem with > the right hemisphere (left visually: I hate radiology ;)), where some dura > seems incorrectly labeled as pial surface (although the grey matter is very > difficult to see on this sequence/ at this setting). > > To fix these I recommend this wiki page: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits > > Good Luck! > Dan > > On 2011 Apr 1, at 05:08 , <freesurfer-request(a)nmr.mgh.harvard.edu> < > freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > > > Send Freesurfer mailing list submissions to > > freesurfer(a)nmr.mgh.harvard.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > or, via email, send a message with subject or body 'help' to > > freesurfer-request(a)nmr.mgh.harvard.edu > > > > You can reach the person managing the list at > > freesurfer-owner(a)nmr.mgh.harvard.edu > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Freesurfer digest..." > > > > > > Today's Topics: > > > > 1. incorrect GM/WM surfaces (Mayuresh K) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 1 Apr 2011 15:21:18 +1100 > > From: Mayuresh K <mayureshk.82(a)gmail.com> > > Subject: [Freesurfer] incorrect GM/WM surfaces > > To: freesurfer(a)nmr.mgh.harvard.edu > > Message-ID: > > <AANLkTi=BLTOKkZngtH5SxhsQvmFrUHakzG9u07Xzworn(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hello freesurfer experts, > > > > I have successfully finished running the recon-all analysis without any > > errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM > > surfaces however look incorrect and I am not sure what may have gone > wrong. > > See attached screenshot from tkmedit. > > Any suggestions how to fix this would be helpful. > > > > I have processed other datasets collected from the same scanner using the > > same sequence which seem to have correctly identified the pial and > > grey-white boundaries. I am using > > freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1. > > > > Thanks, > > Mayuresh > >

2 3

creating labels in tksurfer
by Ilana Hairston 02 Apr '11

02 Apr '11

Hi there, I'm having difficulty creating labels in tksurfer (v4.5). I followed the "Creating Labels" instructions on the Wiki, however clicking Fill on the closed path didn't seem to do anything. I used save label anyway, and tried to load this new label again, and even though it says "7681 nonzero vertices found", again i see nothing. Not quite sure what i'm doing wrong. Also - which LUT file is the correct one to go with aparc.annot? i get the most bizarre labeling with FreeSurferColorLUT Thanks ilana -- ******************************* peligro! flaca pero mala! ******************************

2 3

Vertex-by-vertex analyses within ROIS?
by Dalwani, Manish 01 Apr '11

01 Apr '11

Hello Freesurfers, I am happy to find out that it is possible to carry out vertex-by-vertex analyses for specific ROIs. Can someone help me understand, 1. How to run such a vertex-by-vertex analyses for certain ROI or ROIs? 2. Can we apply cluster-wise correction or FDR to the ROI to correct for multiple comparison? Regards, Manish Dalwani

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add subject to group but cannot find brain for 049
by Knut J Bjuland 01 Apr '11

01 Apr '11

I have added a subject to the to the groups of subject that was available for the qdec tutorials. with this in mind I have used make_average_subject and I have now 41 subject. But when I run this command there is always a subject for which it can not find brain. I am positive that the necessary files are available. The subject that I have add is anonymous mri picture that i have imported into freesurf, and the subject is 20 years old female. Knut J

3 6

preproc-sess OSX bug fix getrunlist
by Juli Dolzhenko 01 Apr '11

01 Apr '11

Hello, I am running into an issue with running preproc-sess on OSX as outlined here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15896.html I saw Doug posted a bug fix that should solve this problem, however, I am unable to access it from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/getrunlist Is there a way I can download this new version of getrunlist? Thanks so much, Juli

4 4

Where can I find long_mris_slopes
by lan lin 01 Apr '11

01 Apr '11

I installed freesurfer 5.0 and want to use long_mris_slopes to prepare the longitudinal data but couldn't find the command. Where can I find it? thanks Lan

2 1

problems with loading a pial surface
by Iris Steinmann 01 Apr '11

01 Apr '11

Hello Freesurfers I still have the problem using a tcl script that should load the pial surface on a patch in tksurfer. I tried to use the following three commands: 1. set gaLinkedVars(vertexset) 3 SendLinkedVarGroup view redraw 2. read_pial_vertex_coordinates redraw 3. read_surface_vertex_set 3 lh.pial redraw But none of them loaded the pial surface. I would be very thankful for a solution ore a hint. Iris

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Re: [Freesurfer] incorrect GM/WM surfaces
by Daniel G Wakeman 01 Apr '11

01 Apr '11

Hi Mayuresh, I assume you are talking about the area in the posterior midline, where the pial surface seems to go 'squiggly'. You also seem to have a problem with the right hemisphere (left visually: I hate radiology ;)), where some dura seems incorrectly labeled as pial surface (although the grey matter is very difficult to see on this sequence/ at this setting). To fix these I recommend this wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Good Luck! Dan On 2011 Apr 1, at 05:08 , <freesurfer-request(a)nmr.mgh.harvard.edu> <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. incorrect GM/WM surfaces (Mayuresh K) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Apr 2011 15:21:18 +1100 > From: Mayuresh K <mayureshk.82(a)gmail.com> > Subject: [Freesurfer] incorrect GM/WM surfaces > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <AANLkTi=BLTOKkZngtH5SxhsQvmFrUHakzG9u07Xzworn(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello freesurfer experts, > > I have successfully finished running the recon-all analysis without any > errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM > surfaces however look incorrect and I am not sure what may have gone wrong. > See attached screenshot from tkmedit. > Any suggestions how to fix this would be helpful. > > I have processed other datasets collected from the same scanner using the > same sequence which seem to have correctly identified the pial and > grey-white boundaries. I am using > freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1. > > Thanks, > Mayuresh >

2 1

incorrect GM/WM surfaces
by Mayuresh K 01 Apr '11

01 Apr '11

Hello freesurfer experts, I have successfully finished running the recon-all analysis without any errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM surfaces however look incorrect and I am not sure what may have gone wrong. See attached screenshot from tkmedit. Any suggestions how to fix this would be helpful. I have processed other datasets collected from the same scanner using the same sequence which seem to have correctly identified the pial and grey-white boundaries. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1. Thanks, Mayuresh

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