Freesurfer October 2011

freesurfer@nmr.mgh.harvard.edu

95 participants
160 discussions

T1 lesions
by Adil Javed 06 Oct '11

06 Oct '11

Hi, Is there any way in tkmedit or freeview to set T1 lesions to background value or to exclude them before recon-all is run so that these lesions do not get misclassified? Thanks, AJ

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Major reg-feat2anat alignment issues along multiple axes
by Michelle Umali 06 Oct '11

06 Oct '11

Hey Freesurfers, I've been trying to register my FEAT data to my Freesurfer data via reg-feat2anat in order to get V1 binary masks: reg-feat2anat --->aparc/aseg2feat --->fslmaths. It seemed to work ok, and I extracted time series for my areas of interest and ran a PPI analysis in FSL. When reviewing my results I discovered that for two people their brains were flipped 90 degrees around multiple axes compared with the group. So I decided to go back to reg-feat2anat and manually edit the registration of all my subjects. For most people the edits were extremely minor. For the 2 highly problematic ones, appropriate rotations were made. When I returned to my PPI analysis, I found that now all of my brains are rotated by at least 45 degrees sometimes about multiple axes. I am thoroughly perplexed. Does anyone know what might have gone wrong? Thanks. Michelle

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qdec and maximum p-value
by Nikolas Borrel-Jensen 05 Oct '11

05 Oct '11

Hi all. I'm using Qdec to compare two groups of patients, and I'm wondering why the vertex with the highest p-value in the clusters changes when the threshold is changed? When lowering the threshold, the significant area should increase, but intuitively, the vertex corresponding to the area with the maximum p-value should remain the same inside the cluster? I'm using the Monte Carlo z-simulation method to remove false positive. Regards, Nikolas

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bug in surface-based area and volume
by Douglas N Greve 05 Oct '11

05 Oct '11

Hi Y'all, I recently found a bug in the way that FS converts surface-based area (eg, lh.area) and volume (eg, lh.volume) into standard space. I'm testing a fix now, but you should not use area or volume measures until I've posted the fix and you re-run either mris_preproc or qcache. The files themselves are fine, it is the way they are transfered to standard space that is the problem. You will not need to re-analyze any of your individual subject data. The volumes of the subcortical structures are unaffected by this problem. Global measures of cortical volume are also unaffected. I'll get back soon (next week) with the fix. Sorry for the inconvenience. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] volume of different lobes of the brain....
by Douglas N Greve 05 Oct '11

05 Oct '11

You will need to run mri_aparc2aseg specifying your lobe annotation as the input (this parcellates WM based on proximity to the annotation). Then run mri_segstats on the output of that to get the WM volumes for each lobe. doug Gonzalo Rojas Costa wrote: > Hi Douglas: > > I was testing the commands that you sent me, but I only got the > cortical volume, but I need the cortical+WM volume of each lobule... > How can I do it ?... > > Sincerely, > > > Gonzalo Rojas Costa > > > > On Mon, Sep 26, 2011 at 11:01 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu> wrote: > >> You can run mri_annotation2label with --lobesStrict to get a lobe >> annotation. If that definition of "lobes" is good for you, then you can run >> mris_anatomical_stats to get the volume for each lobe. >> doug >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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cuda error...
by Gonzalo Rojas Costa 05 Oct '11

05 Oct '11

Hi: I installed CUDA 4 in a Ubuntu 10.10 based workstation... I tried to process a volume, but I got the following error: "writing output transformation to transforms/talairach_with_skull.lta... CUDA Error in file 'gcasgpu.cu' on line 159 : unspecified driver error. registration took 15 minutes and 1 seconds. Abort"... How can I correct it ?... Sincerely Gonzalo Rojas Costa

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Re: [Freesurfer] BOLD time series registration to orig.mgz
by Tessa Dekker 05 Oct '11

05 Oct '11

Hi, I have used bbregister to register a set of partial volume fMRI time series to the subject structural (orig.mgz), which worked very well. I now want to align each volume in each given time series to the orig.mgz. However, I've only managed to get one resampled volume, the target volume, out of bbregister at the time, making the full registration process rather lengthy. I have tried to align my fMRI time series to the orig.mgz by specifying the transformation matrices that I got from bbregister (both register.dat and the fsl compatible flirt.mtx) as input transformation matrix in various afni and FSL alignment scripts. Up until now however, none of my attempts have been successful because all these scripts seem to assume different transformation matrix conventions than bbregister...? Any advice on how to successfully align a whole fMRI time series to a 3D (non-standardised) subject scan, preferably using a bbregister transformation matrix, would be much appreciated. many thanks, Tessa -- Dept. Visual Neuroscience, UCL Institute of Ophthalmology 11-43 Bath Street London EC1V 9EL t.dekker(a)ucl.ac.uk

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Using Freesurfer reg-feat2anat registration to replace original FEAT
by Michelle Umali 05 Oct '11

05 Oct '11

Dear Freesurfers, I've analyzed a run of functional data in FEAT and then used reg-feat2anat to register the FEAT results to the Freesurfer anatomicals. It turns out the original FLIRT registration was bad. When I looked at the reg-feat2anat results, images were flipped 90 degrees. I made edits manually in reg-feat2anat to fix this. How do I feed this corrected registration back into FSL so it can be used instead of the original FLIRT registration in later FEAT analyses? Thanks. Michelle

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upload issues for file drop
by Michelle Umali 04 Oct '11

04 Oct '11

hi Freesurfers, I am trying to upload a 1.4 GB tgz file and I can't register as a new user through Accellion File Transfer. When I try uploading through regular File Drop, the connection times out (because the file is too big?). How can I upload this file? Thanks. Michelle

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funcroi-table-sess with multiple contrasts
by SHAHIN NASR 04 Oct '11

04 Oct '11

Hi, Is there anyway to print multiple contrasts in one output file using funcroi-table-sess command? -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Freesurfer October 2011