Freesurfer October 2006

freesurfer@nmr.mgh.harvard.edu

41 participants
61 discussions

mri_vol2surf error
by Joongnam Yang 12 Oct '06

12 Oct '06

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 --out_type paint and got the following error message, MRISreadCurvature: could not open /home/nam/AVERAGE/average/surf/lh.thickness No such file or directory In the surf directory, I DID find "lh.avg_thickness". Is this an error of Freesurfer? Would someone please let me know how to remedy this? Nam.

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dilating/eroding wm volume
by Bo Shi 12 Oct '06

12 Oct '06

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

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wm and subcortical gray matter volumes
by Bo Shi 12 Oct '06

12 Oct '06

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!

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Intensity/Conversion problem
by Derin Cobia 12 Oct '06

12 Oct '06

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. Also, here's the command I'm using: mri_convert -TI 20 -te 4 -tr 9.7 -flip_angle 0.174532925199433 -ot mgz *subjectid*.img mri/orig/001.mgz Am I doing something wrong? Thanks. -Derin

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setenv FREESURFER_HOME /usr/local/freesurfer
by Juergen Haenggi 10 Oct '06

10 Oct '06

Dear Freesurfer users I am starting to work with Freesurfer, but I have no experience with Unix. For the installation example in the documentation, there is the command: setenv FREESURFER_HOME /usr/local/freesurfer but this command (setenv) could not be found. What happens? What is FREESURFER_HOME? A directory, a file or something else? Thanks for help in advance Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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recon-all error
by Anil Roy 09 Oct '06

09 Oct '06

Hello all, I get the following error when I feed in a dicom file into recon-all. The dicom file is in a directory with 159 other dcm files. Can you please tell me how to rectify this or what the source of the error is. [root@dhcp-129-105-146-217 freesurfer]# recon-all -i /root/Cath/ADULT\ 14-0005-0001-0001.dcm -subjid E001 -sd /usr/local/freesurfer/subjects -all set: Variable name must begin with a letter. Thanks, Anil.

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about ROI
by Lei.Zhang＠uniklinik-freiburg.de 09 Oct '06

09 Oct '06

Hi, Dear FreeSurfers, I'm using FreeSurfer and successfully overlaid the functional activations onto the flatten surface. Now I want to isolate the functional area as ROI and get its average of the amplitude and percent of signal changes in different tasks. I looked up the helpful information in the handbook and Tutorial, but still no ideas. I hopelly someone can give me a guidance about this. Any hints would be appreciated! Thanks, Lei

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corrupted curvature file
by Balaji Lakshmanan 04 Oct '06

04 Oct '06

Dear all, One of our subjects have a corrupted curvature file(lh.curv) due to some overwriting. This subject was reconstructed using older version of freesurfer. I would like to know which step/command should I rerun in order to retrieve this file. Thanks in advance, Balaji

3 2

roisummary and FIR
by Cameron Ellis 04 Oct '06

04 Oct '06

Hi, I am running roisummary with an FIR analysis with a 25s timewindow, 5s prestim and TR=2.5s. I In the summary output I receive 10 nestpercond but shouldn't I receive 11 with these parameters? timecourse: -5.0 -2.5 0.0 2.5 5.0 7.5 10.0 12.5 15.0 17.5 20.0 timepoint: 0 1 2 3 4 5 6 7 8 9 10 I did not mask the roi. If I should only receive 10 nestpercond which timepoint is left out? Thanks in advance. Cameron

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functional overlay onto the occiptal patch with fieldsign
by Lei.Zhang＠uniklinik-freiburg.de 04 Oct '06

04 Oct '06

Hi Dear FreeSurfers, I'm using the new version of FreeSurfer to process retinotopic data. I can view the finial results of eccen, polar and fieldsign on the occiptal patch. Now I want to overlay another block designed activations onto the fieldsign patch with file---load overlay--select the corresponding fsig_000.bfloat---select register.dat---OK, but actually no activations appeared on the patch altough the fsig_000.bfloat can be shown on the overlay layer. Would smeone let me know how to overlay the functional activations onto the retinotopic patch? Thanks in advance! Lei

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Freesurfer October 2006