Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

error loading averaged brain in QDEC
by Ilana Hairston 11 Oct '10

11 Oct '10

Hi there, I am trying to use and averaged subject instead of fsaverage for QDEC. I used make_average_subject to create the new template, which created a folder called avgsubject. Then i ran recon-all -s SUBJECTID -qcache -target avgsubject (on all subjects) In QDEC, in "Common-Space Subject" i typed the new averaged subject folder. But when trying to run analyses, i get an error message: Error in Analyze: Couldn't open file /usr/local/FS5/subjects/FS080920cr/surf/lh.thickness.fwhm10.avgsubject.mgh (where"avgsubject" was the output name of the averaged subject template). Indeed, there are only *h.*.fwhm*.fsaverage.mgh in my subject folders (presumably from the previous preproc), but no new ones with 'avgsubject'. What am i doing wrong? thanks ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Sentimental Insomnia and Nostalgia Disorders Sciences ********************

2 1

password for windows ubuntu to share folders:
by Eggebrecht, Adam 11 Oct '10

11 Oct '10

Hello there, I am using FreeSurfer in my XP box within its Ubuntu Virtual Box. It appears that everything is working just fine. I would like to make changes to the guest OS but need the password to do so. Can I please get this password? I am having trouble mounting my data folders to the guest OS without password or root privileges. Many thanks! -Adam Adam T. Eggebrecht, Ph.D. Dept. of Radiology Washington University School of Medicine St. Louis, MO 314-362-6942 The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

3 5

uniform sampling of the sphere
by Ryan Muetzel 11 Oct '10

11 Oct '10

Hello, I was wondering if there was a way to uniformly parcellate the sphere into "n" regions, and ultimately apply this parcellation to the volume/native space to generate ROIs? Or perhaps output uniformly sampled sphere coordinates that could be converted to voxel coordinates? Thanks in advance! Ryan Muetzel University of Minnesota

2 1

Setting lesion voxels
by Righart, Ruthger Dr. 11 Oct '10

11 Oct '10

Dear Freesurfers, I would like that surface analyses (i.e., cortical thickness) are not confounded by subcortical lesions in patients. Freesurfer provides a work-around in its release notes ( http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) which is to set lesion voxels in brainmask.mgz and norm.mgz to 110 and in aseg.mgz to 77 and then run recon-all -autorecon2-cp (see copy text underneath). As I have lesion masks of every patient I thought it would be best to automatize this step. In that case, I would like to bring mask images with white matter lesions of these patients in the same (freesurfer) space as my T1.mgz, with dimensions 256 x 256 x 256, spacing 1 x 1 x 1., and after that set the lesions to the aforementioned values. Is there a possibility to bring lesion mask of these patients in the same space as T1.mgz in freesurfer? I inspected the function bbregister and mri_convert but could not find a solution here. Any help or suggestions are appreciated! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany Ruthger.Righart(a)med.uni-muenchen.de http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes • mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. A potential work-around is to set lesion voxels in brainmask.mgz and norm.mgz to 110 and lesions voxels in aseg.mgz to 77 (lesion mask can be derived manually or from an automated algorithm), then run recon-all -autorecon2-cp

2 1

{Disarmed} Re: Cluster Multiple Comparison Correction
by Jay Ives 11 Oct '10

11 Oct '10

2 1

Cluster Multiple Comparison Correction
by Jay Ives 10 Oct '10

10 Oct '10

Hi Experts, Which option is best to use: mc-z or perm? I have read that perm gives more accurate results than mc-z, as it uses the actual data rather than fake data to estimate the null distribution. When I use perm, I get no significant clusters. When I use mc-z, almost all clusters are significant. Thanks......J

2 1

Side swapped results?
by Jay Ives 10 Oct '10

10 Oct '10

Hi Experts, I have experienced a possible problem with sided-ness within Freesurfer. I have 2 groups which have been processed through the pipeline without error. I have used the lh.aparc and rh.aparc files to extract parcellated cortex volumes, and analysed the mean differences with SPSS. >From this I get significantly different volumes in the RIGHT fusiform gyrus (amongst others). I then used QDEC to look at vertex based volume differences and found a large significant clusters at the LEFT fusiform gyrus, but not the RIGHT. I'm certain I haven't mixed up the analysis. Can anyone comment on this? Thanks........J

1 0

mri/orig File naming requirements
by Matt Russell 10 Oct '10

10 Oct '10

Hello All, I'm currently working an automation program to setup a FreeSurfer file system for processing. I was wondering if I put a quality check pipeline in the code, deleting files that fail an inspection, would I have problems if the file name order ceased to be 001.mgz, 002.mgz, 003.mgz and was changed to just 002.mgz, 003.mgz? Best, Matthew Russell

3 2

dura flag in fsv5.0.0
by Juranek, Jenifer 08 Oct '10

08 Oct '10

Since the -dura flag is not recognized in FSv5.0.0, how should mempr data (4 echoes) be passed to the latest version of FS? Many Thanks, Jenifer

2 1

Upscaling Functional Data
by Luis Lafer-Sousa 08 Oct '10

08 Oct '10

Using jip-align, we have successfully registered functional data to templates we created from high resolution anatomical scans. To create the templates though, we had to downsample the original scans and lose resolution. Ideally we would like to maintain the resolution of the anatomicals, and upsample the functionals. When trying to do this we run into an error using mri-convert since they are 4-dimensional. How do we upsample the dimensions of functional data? Or how do other groups resolve the resolution differences? Thanks, Luis

1 0

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