Re: [Freesurfer] scuba bus error on MacBook

Aha! Ok. Scuba seems to be working on another intel mac we have that is running tiger and fs 4.0.1, do you think it's worth installing 4.0.1 leopard build, knowing that we won't get any support for it? Or is it likely that I'll run into the same error? Thanks! Akram. > Akram, &

Re: [Freesurfer] scuba bus error on MacBook

into this! Akram. > Will Freeview work for you? Support for scuba has ended because work on > Freeview to replace has been ongoing. > > Nick > > On Wed, 2009-06-10 at 15:24 -0400, ak...@nmr.mgh.harvard.edu wrote: >> Hello, >> I remember I had this same issue last summer

[Freesurfer] scuba bus error on MacBook

ine. Thanks for the help! Akram ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] fslcalc.fsl

Hello, Thanks for adapting fslcal.fsl to work on surfaces Doug. This is very helpful. It was working for me until today. I'm working on thigpen. setenv SUBJECTS_DIR /space/brich_004/users/akram/HRDEV_processing mri_surf2surf --srcsubject 03222007_4TT_clindem47 -

Re: [Freesurfer] mris_calc

-- From: Akram Bakkour Sender: [EMAIL PROTECTED] To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mris_calc Sent: Oct 31, 2008 20:13 Hello, I have two thickness files I want to subtract one from the other, so I did: on thigpen source /usr/local/freesurfer/nmr-std-env cd /space/elvin_005

[Freesurfer] mris_calc

Hello, I have two thickness files I want to subtract one from the other, so I did: on thigpen source /usr/local/freesurfer/nmr-std-env cd /space/elvin_005/users/akram/AGING_MASSIVE setenv SUBJECTS_DIR $PWD mris_surface_stats -mask fsaverage/label/lh.cort_thick.label \ -surf_name

[Freesurfer] Re: [martinos-tech] PAR REC Convert to Analyze or Nifti

, Amy -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] scuba bus error on MacBook

el with Leopard. Thanks! Akram > Akram, > > Which freesurfer distribution was installed? type 'cat > $FREESURFER_HOME/built-stamp.txt' > > What OS do you have? Tiger or Leopard? > > Which processor do you have? Intel or PowerPC? > > Assuming you installed

[Freesurfer] scuba bus error on MacBook

Hello all, We installed freesurfer on a brand new MacBook and downloaded some high resolution MRI data on the hard drive. we can open the volumes in tkmedit but not in scuba, it returns a Bus error. Any ideas? Thanks! Akram. ___ Freesurfer mailing list

Re: [Freesurfer] BrainMaskVol vs BrainSegVol

Total Intracranial Volume (eTIV). Akram Bakkour wrote: Hi all, I want to pull the measure of whole brain volume. In the aseg.stats there is a BrainMaskVol and a BrainSegVol. Which one do I want? As I understand it, BrainMaskVol is the volume of the brainmask (including the ventricles) whereas BrainS

[Freesurfer] BrainMaskVol vs BrainSegVol

including the ventricles, so I think this is the one I want, but I want to make sure and I couldn't find a straight answer on the wiki. Thanks! Akram. -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web:

Re: [Freesurfer] unpacksdcmdir error

I tired setenv UNPACK_MGH_DTI 0 but that unfortunately did not work. I am still getting the same error. unpacking in stable3 seems to work though. Thanks! Akram. On Tue, 4 Sep 2007, Doug Greve wrote: This might be the same problem. Try setenv UNPACK_MGH_DTI 0 and then unpack. I'll t

[Freesurfer] unpacksdcmdir error

f -ot mgz --nspmzeropad 3 --in_type siemens_dicom I get this ERROR: cannot extract sDiffusion.alBValue[1] from 08242007_4TT_clindem93/dicom/00140001 Segmentation fault Any suggestions? Thanks! Akram. -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 0212

Re: [Freesurfer] talairach

it looks good in both dev and std when I check it in tkregister.. I'm assuming it's a problem with tkmedit then? On Tue, 21 Aug 2007, Doug Greve wrote: Have you tried also looking at it with tkregister2? tkregister2 --fstal --s OFRR78 Akram Bakkour wrote: Hi, Is the tala

[Freesurfer] talairach

hanks! Akram. -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] freediffusion dtrecon mask

n on the unpacked data without running diff-flirt, but no luck. Any and all help is highly appreciated. Thanks! Akram. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Talairach problem

Hi, I'm running everything on thigpen. setenv SUBJECTS_DIR /space/thigpen/8/users/akram/ADNI_processing I'm having trouble fixing the talairach of these 4 subjects: 005_S_0572 023_S_0030 116_S_0382 126_S_0405 I've tried: mri_convert brainmask.mgz brainmask.mnc mritotal

[Freesurfer] volume won't load in tkregister (fwd)

Hi, I'm on thigpen and I ran source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/thigpen/8/users/akram/ADNI_processing tkregister2 --mgz --s 023_S_0030 --fstal but no volume will load. Any suggestions? Thanks!

[Freesurfer] Hemispheric devision problem

06_4TTclindem04 check output: foreach s (06142006_4TTclindem03 06212006_4TTclindem04) tkmedit 06142006_4TTclindem03 lh.white -aux wm.mgz -aux-surface rh.white end Notice the hemispheric devision problem with the surfaces. Any suggestions as to how to fix this!

[Freesurfer] freesurfer transformation matrix

much for your help. My very best regards, Akram. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Failed segmentation

the brain and also between hemispheres. wmfill includes the cerebellum as RH even if I set the coordinates for the cutting planes in expert preferences. Any suggestions as to what I should try next? Thanks for the help! Regards, Akram. ___ Freesurfer

[Freesurfer] wm fill won't work with partial brain

e the program continue to make progress rather than fail and stop. Thanks for the help! Akram. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer