Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

mrI_watershed volume segmentation
by slew＠nmr.mgh.harvard.edu 16 Apr '09

16 Apr '09

Hi, I used mri_watershed to get volume segmenstation with -LABEL option. mri_watershed -atlas -LABEL $SUBJECTS_DIR/test/mri/T1.mgz $SUBJECTS_DIR/test/tmp/ What coordinate system is used for the segmented volume ? The coordinate seems a lot different from that of the surface extraction with SRAS. Is RAS coordinate used for the volume segmentation? Is there a way to transform the segmented volume to SRAS ? Thanks, Seok -- Seok Lew, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Building 149, 13th Street, Mailcode 149-2301 Charlestown, MA 02129-2060 USA e-mail slew(a)nmr.mgh.harvard.edu FAX 617 726 7422

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Handling non 1x1x1 voxel size data
by Barkay, Gavriel 16 Apr '09

16 Apr '09

Hi, Apologies if this question is too trivial, or it has already been answered before, but I was unable to figure this out by myself. I have volumes with voxel size 1x1x1.2mm. I was wondering what would be the best way to handle them- Run- mri_convert --confrom ? or- mri_convert --conform_min ? or run the recon-all pipeline on the data with the current voxel size ? or maybe something else? Thanks, Gabi ___ Gavriel Barkay M.D. M.Sc.

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Re: [Freesurfer] Issues with skull stripping
by Bruce Fischl 15 Apr '09

15 Apr '09

Can you send us the 1mm data so we can take a look? Bruce On Wed, 15 Apr 2009, Falk Lüsebrink wrote: > Hi Freesurfers, > > > > Im currently working on four different subjects and Im having problems > with the skull stripping for three of them. The four subjects Im trying to > process are: > > > > 1) 0.6mm iso voxel size, being the same subject as 4) > > 2) 0.5mm iso voxel size > > 3) 0.8mm iso voxel size > > 4) 1mm iso voxel size > > > > The only subject which works nearly perfectly fine is subject 1. > > > > In case of 2 and 3 there are missing parts of the brain or even a whole > hemisphere. I tried using the wsgthresh switch following the tutorial on > the wiki. In case of subject 2 the brainmask.mgz looks fairly good while > setting the threshold to 80, but still some parts of the brain are missing > and setting the threshold to 100 or 150 doesnt change much. There is not > even more skull left. > > > > For subject 3 a threshold of 30 is sufficient and the whole brain is being > shown, though some bits of skull and dura are not removed. I got a good > result for the skull stripping with v4.0.5 by not conforming the data, but I > havent been able to get the same result with v4.3.0. > > > > In case of subject 4 autorecon1 exists with an error during the talairach > check. I tried to follow the wiki for that issue, but havent been able to > even roughly match the movable with the target. So I skipped the tal-check > running into the same problem as subject 2 and 3. > > > > The command lines I used were for subject 1 to 3 recon-all autorecon1 > hires and for subject 4 just recon-all autorecon1. I tried to use > recon-all autorecon1 cm for subject 2 and 3, as this resulted in good > skull stripping using v4.0.5. But recon-all exists with an error during > mri_watershed: GLOBAL region of the brain is empty! I get the same error > if I dont use the no-wsgcaatlas switch during recon-all skullstrip, even > if I didnt use the cm or hires switches before. > > > > As Im not able to reproduce the same results between v4.0.5 and v4.3.0, > have there been made changes to the processes of autorecon1 which I havent > read of affecting the skull stripping? And does anyone have an idea besides > manually doing the skull stripping? > > > > Thanks in advance, > > Regards, > > Falk > >

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Issues with skull stripping
by Falk Lüsebrink 15 Apr '09

15 Apr '09

Hi Freesurfers, Im currently working on four different subjects and Im having problems with the skull stripping for three of them. The four subjects Im trying to process are: 1) 0.6mm iso voxel size, being the same subject as 4) 2) 0.5mm iso voxel size 3) 0.8mm iso voxel size 4) 1mm iso voxel size The only subject which works nearly perfectly fine is subject 1. In case of 2 and 3 there are missing parts of the brain or even a whole hemisphere. I tried using the wsgthresh switch following the tutorial on the wiki. In case of subject 2 the brainmask.mgz looks fairly good while setting the threshold to 80, but still some parts of the brain are missing and setting the threshold to 100 or 150 doesnt change much. There is not even more skull left. For subject 3 a threshold of 30 is sufficient and the whole brain is being shown, though some bits of skull and dura are not removed. I got a good result for the skull stripping with v4.0.5 by not conforming the data, but I havent been able to get the same result with v4.3.0. In case of subject 4 autorecon1 exists with an error during the talairach check. I tried to follow the wiki for that issue, but havent been able to even roughly match the movable with the target. So I skipped the tal-check running into the same problem as subject 2 and 3. The command lines I used were for subject 1 to 3 recon-all autorecon1 hires and for subject 4 just recon-all autorecon1. I tried to use recon-all autorecon1 cm for subject 2 and 3, as this resulted in good skull stripping using v4.0.5. But recon-all exists with an error during mri_watershed: GLOBAL region of the brain is empty! I get the same error if I dont use the no-wsgcaatlas switch during recon-all skullstrip, even if I didnt use the cm or hires switches before. As Im not able to reproduce the same results between v4.0.5 and v4.3.0, have there been made changes to the processes of autorecon1 which I havent read of affecting the skull stripping? And does anyone have an idea besides manually doing the skull stripping? Thanks in advance, Regards, Falk

1 0

Re: [Freesurfer] mri_ca_train parameters?
by Nick Schmansky 14 Apr '09

14 Apr '09

Jamie, The script would contains lines like this: set SUBJECTS=(subj1 subj2 subj3 subj4) set ONE_SUBJECT=(subj3) When rebuilding the atlas of 40 subjects on our cluster, where each subject gets its own node, it takes about 2 days. so on a single machine, about 80 days. Nick On Wed, 2009-04-08 at 16:32 -0500, Jamie Hanson wrote: > > so that it just runs the command locally. note that this script submits > > multiple subjects to multiple nodes, so if you have 30 subjects, and you > > dont use a cluster, it will take much much much longer to complete. > > Hi Nick- > > I am working on that script right now. One quick question about this, > is there an example of the subjects.csh file (to specify files for > training?). I understand I need to set for ONE_SUBJECT variable, but I > wasn't sure how the other SUBJECTS should be specified (and couldn't > find any other examples on-line or in my version of freesurfer). > > RE: computation load / time... It sounds like 2 days w/ multiple > nodes... We don't do any job queue / cluster batching system, so for a > single machine, what is a rough ball-park for completion time? > > Thanks much! > jamie. > > > > > > Nick > > > > > > On Tue, 2009-04-07 at 12:16 -0500, Jamie Hanson wrote: > >> Hi Freesufer folks- > >> > >> I was just about to start constructing a custom aseg atlas and I > >> wondered if there were any recommendations for any of the optional > >> flags? Any parameters yield better results (especially for specific > >> brain regions)? I was focused on improving amygdala segmentation for > >> my structural images (hence my asking). > >> > >> Best, > >> jamie. > >> > >> > >> > >> > > > > > > >

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using freesurfer labels
by amyr＠nmr.mgh.harvard.edu 14 Apr '09

14 Apr '09

Hi Freesurfers, I want to convert a freesurfer label (amygdala aseg) to a ROI (nii file?) that I can use (overlay) in SPM. I ran mri_label2vol and then mri_convert from .mgz to .nii However, the label looks a little off, and I am wondering if I need to do some sort of transformation since Freesurfer works with the Talairach and SPM works with the MNI. In SPM, I registered the BOLD images to the T1 structural image generated in Freesurfer (after running mri_convert .mgz to .img). Does this conversion require a transformation? Thanks for your help. Regards, Amy

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mni152.register.dat
by Yigal Agam 14 Apr '09

14 Apr '09

Hi, Does mni152.register.dat map from fsaverage to mni152 or vice versa? Specifically, I'm using an fsaverage surface that I want to project onto mni152 volume using surf2vol. Should I invert the matrix? Thanks, Yigal

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Re: [Freesurfer] FS-FAST mkanalysis GUI BUG
by Francisco Robles 14 Apr '09

14 Apr '09

Hi Dr. Greve, I am writting to ask you if Free Surfer version 4.3 solves the bug with the mkanalysis GUI you have described us. Please let me know to download this release. Thankfully yours. Francisco Robles Instituto de Nacional de Neurología México _________________________________________________________________ ¿Quieres ordenar tus contactos por grupos? Has clic aquí www.messengernews.com.mx

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dt_recon error about dwi-infodump.dat
by Zhen Zonglei 14 Apr '09

14 Apr '09

Dear Thomas and all: When I processed the DTI data with dt_recon command, I encountered the same problem as the following one you posted in last year. Would you please tell me how to solve the problem? My Freesurfer version is 4.3.0,and MRI data is from Siemens Trio 3T. Attachment is my dwi-infodump.dat. Someone else has an idea? Thanks *Message: 2 Date: Thu, 7 Aug 2008 10:39:11 -0300 From: "MRI CDPI" <**mri(a)cdpi.com.br* <mri(a)cdpi.com.br>*> Subject: [Freesurfer] dt_recon & stage 3 To: <**freesurfer(a)nmr.mgh.harvard.edu* <freesurfer(a)nmr.mgh.harvard.edu>*> Message-ID: <**002601c8f892$f992cbc0$0100a8c0(a)cdpi.local*<002601c8f892$f992cbc0$0100a8c0(a)cdpi.local> *> Content-Type: text/plain; charset="iso-8859-1" Dear group, i am trying to run dt_recon on some dti data, the first two steps: image transformation, eddy_correction, run fine. In the third stage, the glmfit, the process stops after giving the ERROR message: cannot extract sWiPMemBlock.alFree[8] from .../ dwi-infodump.dat And indeed, there is no visible entry of this in dthat dwi-infodump.dat. Somebody has an idea? Thanks for help! Thomas* -- Zonglei Zhen, PhD Assistant Professor of Cognitive Neuroscience BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, P.R. China

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Re: [Freesurfer] aparcstats2table
by Krish Subramaniam 14 Apr '09

14 Apr '09

Hi Falk fsutils is one of the 4 helper scripts missing from the distribution. Please get the 4 scripts from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/datastruct_utils… ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/fsutils.py ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/misc.py ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/subject_info.py And put them in your $FREESURFER_HOME/bin directory. Sorry for the trouble. Krish On Apr 14, 2009, at 10:36 AM, Falk Lüsebrink wrote: > Hi Freesurfers, > > I tried using aparcstats2table today and encountered following error > message: > > Trackback (most recent call last): > File “usr/share/freesurfer/bin/aparcstats2table”, line 6, in > <module> > Import fsutils > ImportError: No module named fsutils > > Is anyone able to offer some help? I am using v4.3.0 and it didn’t > matter if I used any flags or not. > > Thanks in advance, > Falk > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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