Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

Xhemi files do not exist in the specified ftp location
by Negar Memarian 14 Mar '13

14 Mar '13

Dear Doug, Can you please advise me of the correct location of the ftp directories/files required to be installed for surface based interhemispheric registration? I'm trying to download and install the required files from the specified path: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ but the files/folders (e.g., surfreg, mris_preproc , fsaverage_sym.tar.gz , etc) do not exist. I appreciate your help. Regards, Negar

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Process flow: ReconAllDevTable
by Mehul Sampat 14 Mar '13

14 Mar '13

Hi Folks, Based on the tutorials, we normally run full recon-all pipeline; then add control points if required and then run -autorecon2-cp and -autorecon3 again. Recently, I was looking at the process flow table: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable and I have two questions: 1. From this table it seems like ?h.white is created in autorecon2 and ?h.pial is created in autorecon3. However, when i run recon-all -s subj -autorecon1 -autorecon2 i see that ?h.pial is also already created. Does this mean I am interpreting the process flow table incorrectly or is there an error in the table ? 2. Also if ?h.pial and ?h.white are already created at the end of autorecon2; then can we add control points at immediately after autorecon2 ? This way we would need to run autorecon3 only once and save resources. Or am I missing something and is it that one must run -autorecon2 and -autorecon3 and then add control points and then run -autorecon2-cp and -autorecon3 again. Thanks Mehul

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volumetrics questions
by Rashmi Singh 14 Mar '13

14 Mar '13

Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different. I did longitudinal run using the two mprages from same subject, however then also the volumes show differences. May you please advise me what to do. Thanks, Rashmi

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Estimate of number of manual edits and time to complete in 100subject sample
by Schumman Resonance 14 Mar '13

14 Mar '13

This is a question for the FS community in general, I gather there is variability around this, but rather than an exact number and time, I was hoping for an estimate on how many scans would I expect to require manual edits(any of the check points recommended in the tutorials) as well as an estimate of the time it takes to go through them. For the sake of the argument, take a sample of 100 subjects. Thanks, Kev

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Permission denied
by Varghese Chikku 14 Mar '13

14 Mar '13

Dear FS team, I dowloaded the latest ML version of FS and tried to run a subject.But this error is coming up.Any suggestions? chikkuvarghese$ recon-all -i /Users/chikkuvarghese/Desktop/BL/raw/image00001 -autorecon-all -s BL1 mkdir: /Applications/freesurfer/subjects/BL1: Permission denied mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied cp: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/BL1: No such file or directory. chikkus-MacBook-Pro:~ chikkuvarghese$

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Stat doubts
by Gabriel Gonzalez Escamilla 14 Mar '13

14 Mar '13

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convert from vtk to Freesurfer surface file format
by Christine Tardif 14 Mar '13

14 Mar '13

Hello, I would like to use the surface registration tools in Freesurfer. I first need to convert my vtk surfaces into the Freesurfer format. I tried mris_convert, but this seems to only convert from and not to the Freesurfer file format. Does anyone know of another conversion tool available? Thanks for your help, Christine. ___ Christine L Tardif, PhD Postdoctoral fellow Max Planck Institute for Human Cognitive and Brain Sciences Department of Neurophysics www.cbs.mpg.de/~ctardif

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Fwd: 7T Facility Fellow Position in Brisbane
by Douglas Greve 14 Mar '13

14 Mar '13

FYI -------- Original Message -------- Subject: 7T Facility Fellow Position in Brisbane Resent-Date: Thu, 14 Mar 2013 01:01:35 -0400 Resent-From: <DGREVE(a)partners.org> Date: Thu, 14 Mar 2013 04:59:03 +0000 From: Ross Cunnington <r.cunnington(a)uq.edu.au> To: Hello, I'd appreciate if you could pass this on to anyone who may be interested. We're looking for a senior 7T Facility Fellow for our new Siemens 7 Tesla Whole Body MRI system to be installed later this year in Brisbane, Australia. Please see the full job details at: http://uqjobs.uq.edu.au/jobDetails.asp?sJobIDs=494467&lCategoryID=&lBrandID… This is a great opportunity for someone to lead development of the new 7T MRI facility at the University of Queensland (and Brisbane is always sunny). -+- A/Prof Ross Cunnington, Principal Research Fellow Queensland Brain Institute & School of Psychology University of Queensland, Brisbane, Australia Phone: +61 7 3346 6330 Begin forwarded message: From: Rebecca Osborne <rebecca.osborne(a)cai.uq.edu.au<mailto:rebecca.osborne@cai.uq.edu.au>> Subject: 7T Facility Fellow Position at CAI Date: 11 March 2013 9:10:33 AM AEST To: CAI_Staff <CAI_Staff(a)exchange.uq.edu.au<mailto:CAI_Staff@exchange.uq.edu.au>> Cc: Ross Cunnington <r.cunnington(a)uq.edu.au<mailto:r.cunnington@uq.edu.au>>, Stuart Crozier <stuart(a)itee.uq.edu.au<mailto:stuart@itee.uq.edu.au>> Hi All The advertisement for the 7T Facility Fellow position at CAI is now on UQ jobs. The position will be advertised internationally, however please feel free to circulate this link to any professional networks that you feel may be appropriate. http://uqjobs.uq.edu.au/jobDetails.asp?sJobIDs=494467&lCategoryID=&lBrandID… thanks - Bec Rebecca Osborne Deputy Director, Operations Centre for Advanced Imaging The University of Queensland T: +61 7 3365 4235 rebecca.osborne(a)cai.uq.edu.au<mailto:rebecca.osborne@cai.uq.edu.au>

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FS 5.1 MNI305 aparc+aseg registration with FSL MNI152
by raij＠nmr.mgh.harvard.edu 13 Mar '13

13 Mar '13

Dear fellow Surfers, I am trying to overlay FreeSurfer 5.1 MNI305 (=fsaverage) aparc+aseg.mgz 3D volumes (caudate, putamen, pallidum, etc) onto FSL MNI152 2mm resolution volume. I first extract the nuclei from MNI305 aparc+aseg.mgz, for example: mri_extract_label $FREESURFER_HOME/subjects/fsaverage/mri/aparc+aseg.mgz 11 MNI305_3D_masks/mask_lh_caudate.nii I then try to resample the extracted volume into FSL MNI152 2mm space, using the registration that comes with FS 5.1 (.dat format): mri_vol2vol --mov MNI305_3D_masks/mask_lh_caudate.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --o MNI152_3D_masks/mask_lh_caudate.nii Unfortunately, caudate appears in a clearly incorrect location, both when checking the result with tkmedit2, and when viewing the volumes with freeview. Adding --inv does not fix this either. However, if I simply overlay the volume extracted from MNI305 aparc+aseg on the FSL MNI152 2 mm volume, the location looks just fine. It therefore appears that MNI305 and MNI152 are in the same space, and mri_vol2vol is not needed. Is this correct? Or am I just using an incorrect register.dat file? Thanks! Tommi Details: On machine ernie nmr-std-env (5.1.0 stable) $FSLDIR = /usr/pubsw/packages/fsl/current/ $FREESURFER_HOME = /usr/local/freesurfer/stable5_1_0/ --- Tommi Raij, MD, PhD TMS Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Re: [Freesurfer] bbregister error
by Anastasia Yendiki 13 Mar '13

13 Mar '13

Hi Salil - I'm cc-ing Doug who may be able to help. The error happens when bbregister invokes fslregister, in this particular line of fslregister: set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol` When run on brainmask.mgz, it returns "ERROR: could not determine file". a.y On Wed, 6 Mar 2013, Salil Soman wrote: > > Thank you for your email. Changing the mask option got me past the error I > was having initially, but now I get these new errors: > > mri_convert ERROR: could not determine file for > /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis > ter.30396/fslregister/refvol.fslregister.nii > mri_convert ERROR: could not determine file for > /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis > ter.30396/fslregister/refvol.fslregister.nii > > Thank you for your consideration. > > Best wishes, > > -S > > On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Salil - The problem is that you've set dob0 = 1 but you haven't set > b0mlist and b0plist, so it doesn't know where to find your field maps to do > the B0 unwarping. > > a.y > > >

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