Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Resampling NIFTI images
by Antonella Kis 07 Oct '11

07 Oct '11

Dear FreeSurfers, I would like to know if there is a way to re-sample a NIFTI image (obtained after MRIcron conversion, from a dcm image) in Freesurfer with a scale factor of 2. I saw about mri_convert but this doesn't give me any option for the scale factor (for e.g. I want to drop each second slice from my NIFTI image) Thank you. AK

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tracula -bedp - path
by Judit Haasz 07 Oct '11

07 Oct '11

Hi, I ran into 2 problems related to tracula. 1. trac-all -bedp command exits with following message. WARN: Running FSL's bedbost locally - this might take a while >> > WARN: It is recommended to run this step on a cluster >> > bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri >> > subjectdir is /usr/local/freesurfer/subjects/C001/dmri >> > Making bedpostx directory structure >> > Queuing preprocessing stages >> > [: 223: NONE: unexpected operator >> > [: 314: NONE: unexpected operator >> > [: 327: xbedpostx_pre: unexpected operator >> > [: 486: x: unexpected operator >> > [: 486: -le: argument expected >> > Queuing parallel processing stage >> > [: 223: NONE: unexpected operator >> > [: 327: xbedpostx: unexpected operator >> > [: 486: x53: unexpected operator >> > 0 slices processed >> > Queuing post processing stage >> > [: 223: NONE: unexpected operator >> > [: 314: NONE: unexpected operator >> > [: 327: xbedpostx_post: unexpected operator >> > [: 486: x: unexpected operator >> > [: 486: -le: argument expected >> > This problem has been posted in May and June. bedpostx from command line runs perfectly and that is how I have been running it so far. One of u suggested to try the following: /usr/local/fsl/bin/bedpostx_single_slice.sh /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri 2 1 1000 1250 25 1 0 then I got: ** ERROR (nifti_image_read): failed to find header file for '/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000' ** ERROR: nifti_image_open(/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000): bad header info ERROR: failed to open file /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000 ERROR: Could not open image /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000 Image Exception : #22 :: Failed to read volume /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000 An exception has been thrown Failed to read volume /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000Trace: read_volume4DROI. Done Can u suggest a reason behind all this? This happens on Linux machine (2.6.35-28-generic #50-Ubuntu 10.10, x86_64, Java VM Version: Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode). On Mac OS X (version 10.7.1 - Lion, 2 x 2.66 GHz 6-core Intel Xeon processors, 32 GB 1333 MHz DDR3 RAM) trac-all -bedp runs well. My other question is: trac-all -path exists with error (in case of a single subject): Loading DWIs from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri/dwi.nii.gz Loading mask from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri.bedpostX Loading segmentation map from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlabel/mni/aparc+aseg.nii.gz Loading b-values from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri/bvals Loading gradients from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri/bvecs Segmentation fault Linux Odd 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux trac-paths exited with ERRORS at Fri Oct 7 10:21:20 CEST 2011 thanks for help. Judit

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Inaccurate Surfaces Generated
by Jeff Sadino 07 Oct '11

07 Oct '11

Hi Freesurfer Team, When we tried to process some subjects in FS 5.0.0 through the cross-sectional step in the longitudinal processing stream, we got inaccurate surfaces generated. Also, after doing skullstripping or adding control points and re-running the cross-sectional reconstruction, inaccurate pial and white matter surfaces were generated (see attached pictures). We are not sure how to fix this problem and this has affected about 70 of our scans. Several of these subjects we also processed in FS 3 and FS 4.3.1, and the surfaces were generated fine. Are there any known solutions to fixing the surfaces in the newer FreeSurfer? If not, then could we feed the 4.3.1 cross-sectionals into FS 5 to create the base template, and then use FS 5 to create the longitudinal reconstructions? Thank you, Jeff Sadino

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Freesurfer on Neurodebian
by Cartik Sharma 06 Oct '11

06 Oct '11

Hello there, Trying to work with cortical processing software Freesurfer for connectome related stuff. i've installed the s/w on NeuroDebian an debian virtual machine image. I'm getting some OpenGL warnings in running a command >tksurfer bert rh pial OpenGL Warning: vboxcall failed with vbox status code -8 OpenGL warning : SHCRGL_GUEST_FN_WRITE_READ (4543828) failed with *address* Seems like the CPU is still running and computation takes place at run time but results tend to take time to show up.. Is there a particular memory requirement for running Freesurfer on Neurodebian.. Thanks in advance. Cartik

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nonconnexity and holes in parcels
by Ben Hamida Cammoun Leila Faiza 06 Oct '11

06 Oct '11

Hello, I am using freesurfer v5.1.0 (on ubuntu). when processing reconall on my data I notice on the parcellation aparc.annot two strange points: some isolated small regions not annotated, as well as the non connexity of some parcels. I checked the bert aparc.annot on inflated surface and I found the same problem of non connexity, for instance some medialorbitofrontal labeled vertices (vertex index 108562) in rostralanteriorcingulate, or vertex num 103429 labeled as insula in lateralorbitofrontal parcel. In lingual there is also a small hole without annotation like vertices: 35643,36746,37788..... is this normal? if yes, how can we correct that? thanks in advance

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T1 lesions
by Adil Javed 06 Oct '11

06 Oct '11

Hi, Is there any way in tkmedit or freeview to set T1 lesions to background value or to exclude them before recon-all is run so that these lesions do not get misclassified? Thanks, AJ

2 1

Major reg-feat2anat alignment issues along multiple axes
by Michelle Umali 06 Oct '11

06 Oct '11

Hey Freesurfers, I've been trying to register my FEAT data to my Freesurfer data via reg-feat2anat in order to get V1 binary masks: reg-feat2anat --->aparc/aseg2feat --->fslmaths. It seemed to work ok, and I extracted time series for my areas of interest and ran a PPI analysis in FSL. When reviewing my results I discovered that for two people their brains were flipped 90 degrees around multiple axes compared with the group. So I decided to go back to reg-feat2anat and manually edit the registration of all my subjects. For most people the edits were extremely minor. For the 2 highly problematic ones, appropriate rotations were made. When I returned to my PPI analysis, I found that now all of my brains are rotated by at least 45 degrees sometimes about multiple axes. I am thoroughly perplexed. Does anyone know what might have gone wrong? Thanks. Michelle

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qdec and maximum p-value
by Nikolas Borrel-Jensen 05 Oct '11

05 Oct '11

Hi all. I'm using Qdec to compare two groups of patients, and I'm wondering why the vertex with the highest p-value in the clusters changes when the threshold is changed? When lowering the threshold, the significant area should increase, but intuitively, the vertex corresponding to the area with the maximum p-value should remain the same inside the cluster? I'm using the Monte Carlo z-simulation method to remove false positive. Regards, Nikolas

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bug in surface-based area and volume
by Douglas N Greve 05 Oct '11

05 Oct '11

Hi Y'all, I recently found a bug in the way that FS converts surface-based area (eg, lh.area) and volume (eg, lh.volume) into standard space. I'm testing a fix now, but you should not use area or volume measures until I've posted the fix and you re-run either mris_preproc or qcache. The files themselves are fine, it is the way they are transfered to standard space that is the problem. You will not need to re-analyze any of your individual subject data. The volumes of the subcortical structures are unaffected by this problem. Global measures of cortical volume are also unaffected. I'll get back soon (next week) with the fix. Sorry for the inconvenience. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] volume of different lobes of the brain....
by Douglas N Greve 05 Oct '11

05 Oct '11

You will need to run mri_aparc2aseg specifying your lobe annotation as the input (this parcellates WM based on proximity to the annotation). Then run mri_segstats on the output of that to get the WM volumes for each lobe. doug Gonzalo Rojas Costa wrote: > Hi Douglas: > > I was testing the commands that you sent me, but I only got the > cortical volume, but I need the cortical+WM volume of each lobule... > How can I do it ?... > > Sincerely, > > > Gonzalo Rojas Costa > > > > On Mon, Sep 26, 2011 at 11:01 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu> wrote: > >> You can run mri_annotation2label with --lobesStrict to get a lobe >> annotation. If that definition of "lobes" is good for you, then you can run >> mris_anatomical_stats to get the volume for each lobe. >> doug >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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