[Freesurfer] Error with recon-all

Hi, I'm using the version of recon-all that Nick provided at April 17 to be able to run nu_correct prior to the Talairach stage. (I'm on a Mac, OSX 10.6, version v5.1.0). The command given was recon-all -autorecon-all -hippo-subfileds -no-wsgcaatlas \ -clean-tal -s subject. recon-all stopped and

[Freesurfer] file format of patch file (?h.full.patch.3d )

Dear all, I'm trying to access and read a binary patch file (like ?h.full.patch.3d) rather than a converted ascii file. I've found a description of the lay-out of such a file at http://surfer.nmr.mgh.harvard.edu/fswiki/FileFormats that in turn links to http://wideman-one.com/gw/brain/fs/surfacefil

[Freesurfer] Recon-all WARNING: tag image orientation not found

Hi, I'm getting the error WARNING: tag image orientation not found during the mri_convert step of recon-all. The log file is attached here. I am using version freesurfer_v.5.1.0 on Linux RHEL6. I am submitting a job to qsub (command lines in script FSscript3 attached). Any help would be greatly ap

Re: [Freesurfer] Recon-all WARNING: tag image orientation not found

Your dicom file is missing tag 20,37 (the image orientation), which makes it impossible to compute the direction cosines. What is the source of this dicom file? Has it been anonymized? doug On 05/09/2012 12:03 PM, Mary Ellen Koran wrote: > Hi, > > I'm getting the error > WARNING: tag image orien

[Freesurfer] Reading thickness data

Hi all, I'm new to FreeSurfer and I was wondering if there are any methods or software to read the ?h.thickness files and perhaps as a result get a list or table of all the vertices and their corresponding thickness? Also, is there a way to convert the vertex-based thickness files into voxel-based

Re: [Freesurfer] Reading thickness data

Hi Kevin you can use mris_convert to change the thickness to an ascii file by doing (from the surf directory) mris_convert -c thickness ./lh.orig ./lh.thickness.asc you can then sample that back into the volume using mri_surf2vol: mri_surf2vol --surfval ./lh.thickness --hemi lh --fillribbon --

Re: [Freesurfer] Reading thickness data

Hi Kevin, for the first part you can run mri_convert lh.thickness --ascii+crsf lh.thickness.dat For the 2nd part, you can use mri_vol2surf. Like most of our commands, you can run those with -help or --help to get more docs. doug On 05/09/2012 12:53 PM, Kevin Chen wrote: > Hi all, > > I'm new to F

Re: [Freesurfer] Reading thickness data

sorry, that should be mri_surf2vol On 05/09/2012 02:26 PM, Douglas N Greve wrote: > Hi Kevin, for the first part you can run > mri_convert lh.thickness --ascii+crsf lh.thickness.dat > For the 2nd part, you can use mri_vol2surf. > Like most of our commands, you can run those with -help or --help to

Re: [Freesurfer] trac-all -path error

Hi Kiely, Have you checked your inter and intra subject registrations? The control points going off the dwi is not only for one paths but for all the paths. If the registration goes terribly wrong, this can happen. You can take a look at /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registr

Re: [Freesurfer] problems with analysis after using fslmaths

Hi Doug, I have done some more debugging of my analysis and tried different filters. If I understand slxavg-sess correctly, the runs are concatenated, and the pcc is computed over all runs. Is it possible to run a single subject FFX instead (e.g., by uncommenting lines 205-217, 305-310)? Thanks, Ca

[Freesurfer] Entorhinal Ex vivo label

Hi Ruopeng: Is there a command that will allow you to extract the volumes of the EC from the Entorhinal Ex vivo label ? I need to extract this in 77 brain scans. thanks ~ Alan BIDMC/ Boston ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu ht

[Freesurfer] Running recon-all fails during autorecon-2 -careg step

I have run recon-all on multiple subjects and have had it fail at the same step every time with the same error. I am using VirtualBox with the provided Disk Image and Windows 7. 0560: dt=0.001750, rms=0.358 (0.039%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error.

Re: [Freesurfer] Running recon-all fails during autorecon-2 -careg step

Hi Cyrus, it's almost certainly running out of ram. How much do you have in that machine/VirtualBox? Bruce On Wed, 9 May 2012, Sarosh, Cyrus wrote: I have run recon?all on multiple subjects and have had it fail at the same step every time with the same error. I am using VirtualBox with the

[Freesurfer] Entorhinal Cortex

Hi Imagers: Is there a command that will allow you to extract the volumes of the EC from the Entorhinal Ex vivo label ? I need to extract this in 77 brain scans. thanks ~ Alan BIDMC/ Boston ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu ht

[Freesurfer] recon-all error

Hello, I ran recon –all on my scans and the output files reported the following error: SUBJECTS_DIR /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer FREESURFER_HOME /opt/freesurfer Loading source label. Invalid argument ERROR reading /home/rsingh/storage/labs

Re: [Freesurfer] file format of patch file (?h.full.patch.3d )

Hi Cris I don't think it's changed, but you could use one of our interfaces (matlab or C) to read it if you want to be forwards-compatible. cheers Bruce On Wed, 9 May 2012, Cris Lanting wrote: Dear all, I'm trying to access and read a binary patch file (like ?h.full.patch.3d) rather than

Re: [Freesurfer] problems with analysis after using fslmaths

Hi Doug, I have done some more debugging of my analysis and tried different filters. If I understand slxavg-sess correctly, the runs are concatenated, and the pcc is computed over all runs. Is it possible to run a single subject FFX instead (e.g., by uncommenting lines 205-217, 305-310)? Thanks, Ca

[Freesurfer] optseq2 and tnullmin/max

Dear list, I have an optseq2 question, and would very much appreciate your time. I'm having difficulty calculating the required number of timepoints. I'd like to use --tnullmin and --tnullmax so as to have a null event in between each trial, with a duration of 4-8 sec. I have 16 conditions, 6 r

Re: [Freesurfer] longitudinal study in counterbalance design

In terms of just giving it a name, it should not matter since all of the time points are treated equally in the longitudinal stream. When you go to analyze it, the order will make a difference (and I assume you'll use phase). doug On 05/07/2012 11:59 PM, lordowen wrote: > Hi all: > > We performed

Re: [Freesurfer] problems with analysis after using fslmaths

You can run selxavg3-sess with -per-run and it will give you a different output for each run. These results can then be combined in a fixed effects analysis using mri_glmfit. doug On 05/09/2012 03:09 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > I have done some more debugging of my analysis and

Re: [Freesurfer] optseq2 and tnullmin/max

Hi Hanah, I just found and fixed the bug. It was making the effective tNullMax = tNullMin + your specified tNullMax. I've put a new (linux) version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2.linux doug On 05/09/2012 06:09 PM, Chapman, Hanah wrote: > Dear list, >

[Freesurfer] DOSS, thresholding and thresh-sign questions

Dear all I'm fairly new to Freesufer and have started a cortical thickness group analysis. I had a few doubts/questions which I found most the answers for on previous emails on the FS archives - thank you! But I have a few more questions, I hope one of the FS experts can help me out. I will bri

Re: [Freesurfer] Poor Cortical Reconstruc​tions in Pediatrics

Hi xin If you upload one, we will take a look Bruce On May 9, 2012, at 8:57 PM, Xin Zhang wrote: > Hello FreeSurfers, > > Please ignore the previous email. This one includes an example picture. > > We are processing about 100 pediatric subjects ages 3-9 using FreeSurfer > 5.1.0. For som

Re: [Freesurfer] recon-all error

recon-all is supposed to create a symlink from the fsaverage in your /opt/freesurfer/subjects dir to you subjects dir, but sometimes this doesnt seem to work for some people. so first goto your subjects dir and check if that link is there (could be a broken link). if it isnt, then just copy the f

Re: [Freesurfer] Error with recon-all

Hi Nick, Apologies, I should have looked at the recon-all.log file myself. It says that there was an error with mris_topo_fixer: it couldn't allocate memory (malloc error). So I guess that the brainmask is still not correct. I will try to fix that with the option -wsmore. Cheers, Ed On 9 May 201