[Freesurfer] Interpretation of voxel values in TRACULA "path.pd" images

2012-11-09 Thread Jon Clayden
Dear all, I understand that the various "path.pd" image files that are created by TRACULA represent a posterior distribution over the corresponding tract location, but I was wondering if someone could explain to me exactly what the values in these images mean. I assume that they are not probabilit

Re: [Freesurfer] Interpretation of voxel values in TRACULA "path.pd" images

2012-11-09 Thread Anastasia Yendiki
Hi Jon - The path.pd volumes are indeed the posterior probability distributions of each pathway. They are not normalized to a sum of 1 though b/c they're estimated by a sampling algorithm (drawing sample paths from this unknown distribution and adding up the sample paths, instead of estimating

[Freesurfer] pre-processing functional data error

2012-11-09 Thread Yangmei LUO
Hi there, I am a newbie and I used data collected from SIEMENS 3T to practice. It works well when I tried to preprocess structural data using freesurfer. However, there is a problem when I tried to convert the functional data in DICOM into NII using freesurfer. The problem I can not solve, so I t

Re: [Freesurfer] pre-processing functional data error

2012-11-09 Thread Douglas N Greve
Are they straight off of the scanner or did you anonymize them? Can you send me one of the dicom files? doug On 11/09/2012 11:39 AM, Yangmei LUO wrote: > > Hi there, > > > I am a newbie and I used data collected from SIEMENS 3T to practice. > It works well when I tried to preprocess structural d

Re: [Freesurfer] checking talairach.lta

2012-11-09 Thread Douglas N Greve
yes, that info will be helpful doug On 11/09/2012 03:46 AM, Knut J Bjuland wrote: > Could you please send the information in /etc/redhat-release or the > first lines when you start dmesg |less to the list. Do the cluster > have Ubuntu or Redhat Linux? > > Knut J Bjuland > > On 08. nov. 2012 20:

Re: [Freesurfer] Interpretation of voxel values in TRACULA "path.pd" images

2012-11-09 Thread Jon Clayden
That does help - many thanks! Jon On 9 November 2012 15:56, Anastasia Yendiki wrote: > > Hi Jon - The path.pd volumes are indeed the posterior probability > distributions of each pathway. They are not normalized to a sum of 1 though > b/c they're estimated by a sampling algorithm (drawing sampl

Re: [Freesurfer] Error in recon-all after updating mri_segstats.

2012-11-09 Thread Douglas N Greve
Use this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux doug On 11/08/2012 10:01 PM, Zheng Hui wrote: > Hi Doug, > > After updating the mri_segstats, all our recon-all encounter errors as > follow log suggest. Please advice a work around. > > Thank you, >

Re: [Freesurfer] source of recon-all errors?

2012-11-09 Thread Douglas N Greve
Oh, sorry, you have an updated but buggy version of mri_segstats. Try the version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux doug On 11/09/2012 12:44 PM, Angie Morales wrote: > Here is my log file. Thanks again. > > On Thu, Nov 1, 2012 at 5:04 PM, Angi

Re: [Freesurfer] checking talairach.lta

2012-11-09 Thread Douglas N Greve
Oh, you have CentOS4, try this version instead ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2.bin.centos4.0_x86_64 doug On 11/09/2012 02:23 PM, Eric Cunningham wrote: > thanks for the tip knut. > it appears to be redhat CentOS release 4.6 > -eric > > On Fri, Nov 9, 201

[Freesurfer] Qdec - longitudinal. File missing

2012-11-09 Thread Alex Hanganu
Dear FreeSurfer Experts, we performed the long_mris_slopes cmd and finished without error. According to the "Longitudinal Processing Tutorial", we created after that the cross sectional form of the qdec table, and then the qdec/.Qdecrc file. When running the qdec analyses, we receive an error:

[Freesurfer] ASCII .curv format viewing problem

2012-11-09 Thread Sourena Soheili-Nezhad
Hello Freesurfer expert community I have been analyzing the jacobian values outside freesurfer by exporting it to ascii format. Now, I have come up to vertex-wise statistical values which I wish to project on the study surface. Reading the list, I have created an ascii with each row representing <#

Re: [Freesurfer] ASCII .curv format viewing problem

2012-11-09 Thread Bruce Fischl
Hi Sourena there are matlab scripts for reading/writing curv files, but you are probably better off stuffing things into a "volume" and saving it in .mgz format using MRIwrite.m cheers Bruce On Sat, 10 Nov 2012, Sourena Soheili-Nezhad wrote: > Hello Freesurfer expert community > I have been an

Re: [Freesurfer] Qdec - longitudinal. File missing

2012-11-09 Thread Martin Reuter
Hi Alex, check the bases of other subjects. Are there any fwhmfsaverage files? Did you run with the --qcache flag? Then these should have been created. Maybe you passed a specific fwhm value different from 10? Best, Martin On Fri, 2012-11-09 at 17:13 -0500, Alex Hanganu wrote: > Dear FreeSu

Re: [Freesurfer] Qdec - longitudinal. File missing

2012-11-09 Thread Alex Hanganu
Hello Martin, thanks for your answer, I used the --qcache. The cmd was: long_mris_slopes --qdec qdecfile --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time months --fwhm 10 --qcache fsaverage --sd SUBJECTS_DIR All the bases subjects have the specific f