Siti, can you give us the full command-line (without the variables) and the full terminal output?
doug
Siti Hajar wrote:
When I ran this command, " mri_segstats --seg "$fsaveragesurfpath"/"$hemi".fsaverage."$hemi"_"$roi"_"$subj".mgh --in "$hemi".thickness.fsaverage.mgh --sum segstats-"$hemi"_"$roi"_"$subj".txt, this kind of output came out "mghRead(/usr/local/freesurfer/subjects/100905lsy/surf/lh.thickness.fsaverage.mgh, -1): could not open file--> which indicated that there was no lh.thickness.fsaverage.mgh created. Well, basically, when I ran recon-all, lh.thickness.fsaverage.mgh should be created, but it wasn't. So, again with my question,is this situation happened due to the new freesurfer software that I installed or was it caused by other source? The skull strip result was ok
*From:* "freesurfer-request@nmr.mgh.harvard.edu" freesurfer-request@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Mon, September 20, 2010 9:49:16 PM *Subject:* Freesurfer Digest, Vol 79, Issue 32
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Today's Topics:
- Re: mri_label2volume issues (Michael Waskom)
- Generating a 'non-zero' group mask (Marco Loggia, PhD)
- Re: recon-all quality control checks on large numbers of subjects (Nick Schmansky)
- lh.thickness.fsaverage (Siti Hajar)
- Re: lh.thickness.fsaverage (Douglas Greve)
Message: 1 Date: Fri, 17 Sep 2010 11:04:00 -0400 From: Michael Waskom <mwaskom@mit.edu mailto:mwaskom@mit.edu> Subject: Re: [Freesurfer] mri_label2volume issues To: Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu Message-ID: <AANLkTi=5ZnihXybQu0Wwf-ysJN6oPoQk2bFuf2_iirzb@mail.gmail.com mailto:5ZnihXybQu0Wwf-ysJN6oPoQk2bFuf2_iirzb@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1
Hi Prapti,
Basically, you just need to have a label file that you can turn into a lh.your_annot_name.annot (assuming your actual ROI is in the right hemisphere), so that mri_label2annot runs properly.
The easiest thing to do would be to rename any old label you have in your subject's label directory to lh.dummy.label, and then create an annotation from that label with mri_label2annot. Then run mris_aparc2aseg as you tried to do before, which will create a volume that has 0's everywhere except in the area where your actual and dummy labels were projected. Figure out the voxel values for the ROI you want (using Freeview or tkmedit), and then run:
mri_binarize --i your_annot_name+aseg.mgz --match <that voxel value> --o you_roi_name.mgz
Which will have 1s where your ROI is and 0s everywhere else.
Best, Mike
-------Original Message-------
Hi Doug, Thanks for the reply. I am sorry, I am a bit confused about what you mean by creating a dummy label. I am also not sure at which step I need to do this.
As I understand it, I use mri_label2annot to transform my label into a annotation file and this will be separate for the two hemispheres. Do I then edit these files ? where exactly do I use mri_binarize?
Thanks,
Prapti
-----Original Message----- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu] Sent: Friday, 17 September 2010 12:44 AM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2volume issues
Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The
easiest thing is to make a dummy label for the other hemisphere. In the final segmentation, left hemisphere will have an index of 1000+something, the right will have 2000+something. You can then use mri_binarize with --match create a new binary volume with just your hemisphere.
doug
Prapti Gautam wrote:
Hi Doug,
Thanks for the reply. I have tried using the method you've suggested, however, I'm stuck because mri_label2annot which I use to turn my
label
into a annot file only works in one hemisphere while mri_aparc2aseg works for the whole brain. Do you know a work around for this?
Can I merge the annot files created from each hemisphere so that I can pass it to mri_aparc2aseg?
Thanks,
Prapti
Message: 2 Date: Fri, 17 Sep 2010 11:38:22 -0400 From: "Marco Loggia, PhD" <marco@nmr.mgh.harvard.edu mailto:marco@nmr.mgh.harvard.edu> Subject: [Freesurfer] Generating a 'non-zero' group mask To: <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: 5EA6CF4FA3914BC49D4CC51BD03A8618@MARCOWORK Content-Type: text/plain; charset="us-ascii"
Dear all,
I am performing surface analyses on ASL CBF maps. As these maps do not cover the whole brain, and some masks have larger brain coverage than others, I would need to create a binary surface mask (in the fsaverage space) which would zero out the vertices where at least one of my subjects have a zero value. This map would then be used to spatially limit my statistical analyses in mri_glmfit.
Any suggestions?
Thanks a lot,
Marco
Marco L. Loggia, PhD
Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital
Harvard Medical School
CNY Building 120, suite 101E
Charlestown, Massachusetts 02129
Phone: (617) 643-7267
Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu mailto:marco@nmr.mgh.harvard.edu