Re: [Freesurfer] mri_convert on 64bit vs 32bit

Hi Nick, Thanks for the response. They are from a Philips machine though... Niels On 10/12/06, Nick Schmansky <[EMAIL PROTECTED]> wrote: Niels, Are they Siemens Dicom files? If so, try adding the flag -siemens_dicom to mri_convert. This wouldn't explain the difference in behavior between the

Re: [Freesurfer] mri_convert on 64bit vs 32bit

Niels, Are they Siemens Dicom files? If so, try adding the flag -siemens_dicom to mri_convert. This wouldn't explain the difference in behavior between the 32bit and 64bit builds though. I have not personally encountered the message you are seeing. Nick On Thu, 2006-10-12 at 16:40 -0400, Niel

[Freesurfer] mri_extract_label

Hi everyone, My goal is to have the cortical segmentation in subject's native space in analyze format volume images. the series of commands i run are: mri_extract_label aparc+aseg.mgz LABELNUM outVolume.mgz mri_convert -rt nearest -rl rawavg.mgz outVolume.mgz outLabelSegmentation.img the probl

Antwort: Re: [Freesurfer] func2roi-sess error?

Hi Nick, It's working now! Thanks! Lei Nick Schmansky <[EMAIL PROTECTED] rvard.edu>

Re: [Freesurfer] func2roi-sess error?

Lei, It looks like a bug in func2roi-sess. To fix it, open with a text editor this file: $FREESURFER_HOME/fsfast/bin/func2roi-sess and delete the following line: set V2R = ~greve/sg1/build/mri_vol2roi/mri_vol2roi The line following it should read: set V2R = mri_vol2roi which is corre

[Freesurfer] mri_convert on 64bit vs 32bit

Hi, I am experiencing quite a strange problem. I have a set of DICOMs that when I run the following on a 32bit machine, it works fine: mri_convert 031G0110.101.dcm 001.mgz When I run the exact same command (from within the same directory) on the 64 bit machine, I get the following error: "Curren

[Freesurfer] mri_vol2surf error

Dear all, I am trying to overlay group-averaged data (FSL) on an averaged anatomical brain (Freesurfer). I did the following, mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh --projfrac 0.5 --out AVG.gfeat/cope1.feat/thresh_zstat1-lh.w -

[Freesurfer] func2roi-sess error?

Hi All, I tried func2roi-sess with my data, it ran quickly and gave one message at the end 'Unknow user: greve', but no other errer reports. I checked the sessid directory and found it created the -roisef directory, but no files in it. I think there must be something wrong, associated with user? An

Re: [Freesurfer] dilating/eroding wm volume

Hi Bo, you can use flags to mri_segment to change the intensity thresholds: -wlo <>specify the min allowable value for white matter -ghi <>specify the max allowable value for gray matter -glo <>specify the min allowable value for gray matter On Thu, 12 Oct 2006, Bo Shi wrote: Good

[Freesurfer] wm and subcortical gray matter volumes

I didn't want to clutter up one thread with two unrelated questions; Is there a quick way to get a total count for wm/gm volume and subcortical gray matter? AFAIK, the output is divided into a much finer structures... Thanks! ___ Freesurfer mailin

[Freesurfer] dilating/eroding wm volume

Good morning! I have a dataset whose white matter volume is a bit too aggressive and I'd like to erode it a bit - is there a quick way to do this using tkmedit or one of the command line tools? Thanks, Bo ___ Freesurfer mailing list Freesurfer@nmr

Re: [Freesurfer] Intensity/Conversion problem

oh, I take it back, you shouldn't have to conform at that stage. What does the orig.mgz look like? It is 0-255, and the thing you want to avoid is saturation of the intensities. It tries to put the bulk of the histogram in the mid intensity range. On Thu, 12 Oct 2006, Derin Cobia wrote: I se

Re: [Freesurfer] Intensity/Conversion problem

try specifying -conform also. On Thu, 12 Oct 2006, Derin Cobia wrote: I seem to be having some difficulty in converting my flash images into FS format for processing. After using mri_convert my orig.mgz files become excessively bright compared to the original analyze file, thus creating poor au

[Freesurfer] Intensity/Conversion problem

I seem to be having some difficulty in converting my flash images into FS format for processing. After using mri_convert my orig.mgz files become excessively bright compared to the original analyze file, thus creating poor autorecon1 output, etc. See the attached jpgs of before and after shots.