Hi Melonee, Please record my off Campus work hrs this morning at OU. IN 9:30 AM and out 1:10 PM. I have logged into LIBR when I entered so that should be in records. Let me know if you may have any question. Thanks, Rashmi

On 2/11/13 8:39 AM, "freesurfer-request@nmr.mgh.harvard.edu" freesurfer-request@nmr.mgh.harvard.edu wrote:

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Today's Topics:

1. A question regarding a "nii-read" error I get when running a script for FA values output (Rotem Saar)
2. re conversion (Linn Mittlestein)
3. LME matlab toolbox - smooth error (Yolanda Vives)
4. thickness and area in aparc.stats and mri_glmfit (Wolff Schlotz)
5. trac-all -path error (stdp82@virgilio.it)
6. R: trac-all -path error (stdp82@virgilio.it)
7. Re: re conversion (Bruce Fischl)
8. Antw: Re: thickness and area in aparc.stats and mri_glmfit (Wolff Schlotz)

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Message: 1 Date: Mon, 11 Feb 2013 11:50:15 +0200 From: Rotem Saar saar.rotem@gmail.com Subject: [Freesurfer] A question regarding a "nii-read" error I get when running a script for FA values output To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAMjFEmY3_B2G7VVqeGTcptYmS4cdAAdgbka6UTR=-1W_p=G7JQ@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"

Hi,

My name is Rotem, I'm a PhD. student and recently started to work with freesurfer software (freesurfer-Linux-centos4-stable-pub-v5.1.0). QUESTION For several weeks, I have been trying to operate a script for FA values, with no success, and would really appreciate your help with shading some light regarding the problem and it's solution. I have a data set, after an anatomical segmentation (file is attached, named "Anatomical segmentation for fs", this is the script I'm using for brain anatomical segmentation). What I'm trying to run now is the DTI script, in which I run commands that at least for my understanding spouse to give me at the end a table with all the FA values for each brain region (ROI). The script I'm using to do this is attached and called "DTI_RUN_NEW_FOR_FS". *After running phase 5*, in which a mask file should be created (indeed I have checked and the file is created in the same folder it should be):

fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_mask /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii /usr/local/freesurfer/subjects/FOLDER_NAME/mri/brainmask.mgz /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii DoAbs = 0 Found 16777216 voxels in mask Writing masked volume to /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii...d one.

*I run phase 6, and then get the following error message:*

fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii --sum /usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME

$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --i usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii --sum /usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME sysname Linux hostname fmri4-P67A-D3-B3 machine i686 user fmri4 Loading /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz Loading usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii niiRead(): error opening file usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii ERROR: loading usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii

I think the problem is between phase 5 and 6, and is related to file format (.nii) but don't have a hint regarding what can I do to solve this:( Can someone please write me the correct code line ?

I would really appreciate your kind help since I run out of ideas for solutions.

Thanks in advance,

Rotem