Freesurfer April 2009

freesurfer@nmr.mgh.harvard.edu

80 participants
131 discussions

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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aparcstats2table
by Falk Lüsebrink 14 Apr '09

14 Apr '09

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 didnt matter if I used any flags or not. Thanks in advance, Falk

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total brain volumes
by Dankner, Nathan (NIH/NIMH) [F] 13 Apr '09

13 Apr '09

I am looking to derive total brain volume measures from the data that I have. Judging by reading previous posts, it seems that BrainSegVol in aseg.stats includes cerebellum and ventricles. Is there any way to eliminate these from the calculation? Is it kosher to subtract the cerebellum/ventricle measures found elsewhere in aseg.stats/wm.parc from BrainSegVol, or are these derived differently from BrainSegVol? Secondly, would merely adding the left-cerebral-cortex to right-cerebral-cortex measures found in aseg.stats give me total brain volume? Thank you in advance, Nathan

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detecting movement artifact
by karlkarl 13 Apr '09

13 Apr '09

Hello, freesurfer experts We are doing the structure scan on the adolescents. One potential problem is the head movement from the participants. But so far from the image, it looks ok. The question is 1 What is the visual check after autorecon3? We did the visual check after autorecon1 and autorecon2 to examine the skull stripping and pial/white surface. 2 Even freefurfer finished without error after all the recon-all steps, does it mean the data is of good quality. Is there any way in freesurfer to do a quality assessment of the image? Thanks a lot! _________________________________________________________________ Live Search视频搜索，快速检索视频的利器！ http://www.live.com/?scope=video

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3D visualization of subcortical volumes
by Alexa Nardelli 11 Apr '09

11 Apr '09

Hi, I have used FreeSurfer volumetrics to obtain various volumes of some subcortical structures. I would like to obtain a 3D image of each of these subcortical structures. I have tried importing the volumes into Matlab, however Matlab doesn't recognize the mgz file. Any suggestions on how I could go about doing this? Thanks, Alexa

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Re: [Freesurfer] Two problems.
by gmszh 10 Apr '09

10 Apr '09

Hi Bruce, Thanks for the reply. So I will do recon-all -talairach for all subjects using version 4.30 and obtain the new eTIV, keeping the segmentation and surface data unchanged. Is that the correct way? And can someone please help me with problem #1? Thanks, Zheng Hui On 8/4/09 20:51, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Zheng, > > I'll leave 2 for Nick. As for 1, we don't use the tal very much, and a > bad tal will not affect your thickness estimates. The newer versions > rarely have a bad tal since we changed over to Avi Synder's code (which > also fixes the problems we had with eTIV). You can manually correct it > using tkregister2, although this is probably only needed if you want to > report tal coords (or average in tal space). > > cheers, > Bruce > > On Wed, 8 Apr 2009, gmszh wrote: > >> Hi all, >> >> I have two problems here. >> >> 1. talairach.xfm >> By browsing through the mailing list, it seems that talairach.xfm was >> not used much in the recon-all process which is quite different from the >> table given at >> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps. We did find >> many subjects with bad talairach transformation but reasonable segmentation >> and surface reconstruction (version 3.05). Are the results (volumes and >> cortical thickness) for those subjects still trustworthy? Can you kindly >> clarify the importance of talairach.xfm in the pipeline? And since the new >> method of eTIV uses this transformation, is there any way to ensure manual >> registration is fine enough to be used for this estimation, if I have to >> manually register those subjects mentioned above? >> >> 2. recon-all -long >> We processed our data with the longitudinal pipeline. So far we only >> found 6 subjects failed among 200 subjects (tp1 corrected). All these 6 >> subjects seemed to have problem during the registration from tp2 to tp1. I >> used the command "tkmedit -f tp2.long.tp1/mri/orig.mgz -aux >> tp2.long.tp1/mri/orig_tp1_to_tp2.long.tp1.mgz" and realized they were not >> aligned. I have tried different cost functions using >> "fsl_rigid_registration". All of them gave the same result. Is there any way >> I can do the manual registration? I used "fsl_rigid_registration" because no >> matter which cost function I specified to recon-all -long, it would call >> "fsl_rigid_registration" with corratio as the cost function. >> >> Thanks in advance, >> Zheng Hui >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>

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Freesurfer April 2009