Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

how to threshold a sig.mgh file and binarize?
by Burzynska, Aga 31 Aug '11

31 Aug '11

Dear experts, I cannot find a simple way to threshold my sig.mgh file from a functional group analysis (the file is in the fsaverage space). I would like to binarize it and save as a mask to use it with the --mask flag in the mri_glmfit command (to restrict other analyses to these parts of the cortex. I will be very grateful for your help! Cheers, Aga

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Re: [Freesurfer] mris_ca_label
by Haitao Ge 31 Aug '11

31 Aug '11

Hi Bruce, I want to check the results and do some edit if possible. What is the possible reason? Thanks, Haitao

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mris_ca_label
by Haitao Ge 30 Aug '11

30 Aug '11

2 1

Periaqueductal gray ROI
by Ritobrato Datta 30 Aug '11

30 Aug '11

Hi All, Is there a Periaqueductal Gray ROI generated by freesurfer recon ? Please let me know. Thanks Ri

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bad pial surfaces
by Reza Farivar 30 Aug '11

30 Aug '11

Hello, I've been banging my head against the wall and keyboard to get mris_make_surfaces generate correct pial surfaces. While the white matter surface looks okay for the most part, the pial matter surfaces almost never actually reach the pial surface, but rather stop very close to the white matter surface. I was able to get it pushed out a bit by setting MIN_GRAY_AT_CSF_BORDER and MAX of that same parameter to really low numbers, but then it makes the error of putting the pial surface somewhere in the csf. Is there a list of parameters that I can play with to correct this problem? I should note that I'm working with macaque MRI's acquired at 0.35mm iso that have been made to look like they were acquired at 1mm in order to make freesurfer happy. If there is a thickness limit to gray matter, then this may fail at some locations because of the incorrect voxel size. Is there such a limit set in mris_make_surfaces? Many thanks in advance for your help, Reza

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Freesurfer surfaces in the original space
by Navid Shiee 30 Aug '11

30 Aug '11

Dear Freesurfer team, I have a question regarding Freesurfer surfaces. I submitted this questions to the wiki but did not get any response and I was wondering if you can help me on this issue. I am doing some experiments with Freesurfer and would like to have surfaces in the original image space. FS converts everything to 1mm^3 256x256x256 grid in the coronal space. I have axial images which does not have homogenous grid (although it has isotropic resolution). I know there is a command to convert the volumetric structural segmentation into the original space but could not find the command for surfaces. I would be very grateful if you can provide me with some information for doing this. I appreciate your kind help in advance. Regards, -- Navid Shiee Ph.D. Candidate Laboratory of MEDical Image Computing (MEDIC) Image Analysis and Communication Laboratory (IACL) Johns Hopkins University

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Error with dt_recon
by Antonella Kis 30 Aug '11

30 Aug '11

Dear All: I am running the dt_recon:# setenv FREESURFER_HOME /usr/local/freesurfer # setenv SUBJECTS_DIR $FREESURFER_HOME # cd /usr/local/freesurfer/NPI001 # dt_recon --i /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti and I am getting the following error: ERROR: cannot extract sDiffusion.alBValue[1] from /usr/local/freesurfer/NPI001/dti/dwi-infodump.dat Can someone help, please? Thank you. AK

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mri_convert jpeg compression error
by dehaes＠nmr.mgh.harvard.edu 30 Aug '11

30 Aug '11

Dear Freesurfer developers and users, I experience error converting .dcm to .nii with mri_convert these days. I do not know why because it is not reproducible and error occurs mostly with new scans (MPRAGE and other functional sequences) from a Siemens Trio Tim 3T. Here is a display output as an example when I type : mri_convert IM-0001-0001.dcm anat.nii mri_convert IM-0001-0001.dcm anat.nii $Id: mri_convert.c,v 1.171 2010/09/14 21:03:12 greve Exp $ reading from IM-0001-0001.dcm... Getting Series No Scanning Directory INFO: Found 106 files in /Users/dehaes/Work/Research/ASL/CHB/Data/Siemens_pasl/4503697/Anat INFO: Scanning for Series Number 5 INFO: found 104 files in series INFO: loading series header info. INFO: sorting. RunNo = 4 INFO: (192 192 104), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 0.964 -0.234 -0.129 -6.753; 0.238 0.971 0.015 7.906; 0.122 -0.045 0.992 -5.687; 0.000 0.000 0.000 1.000; ERROR: the pixel data cannot be loaded as it is JPEG compressed. (Transfer Syntax UID: 1.2.840.10008.1.2.4.70) Does Siemens recently changes the way they write DICOM from the console? Do you guys know how to avoid this error? Thanks Mathieu Dehaes

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mri_convert -conform issue
by Sebastian Moeller 29 Aug '11

29 Aug '11

Hi List, I just noticed that when I use mri_convert -conform (which reslices my RPI volumes to LIA) the tkrvox2vras matrices seem not to change (for both freesurfer centos4 64bit, version 4.5 and version 5.1). I use MRIread to read in the resulting files in matlat and try to compare the volumes there. All the vox2ras are changed by the conformation (as I expect), but the tkrvox2ras of the conformed volume equal the tkrvox2ras matrix from the original volume. I am confused now as the tkrvox2ras and the x_r, x_a, x_s, (as well as the y_* and z_*) vectors are updated and match the vox2ras matrices. Shouldn't tkrvox2ras also be updated? And if not why :) ? Best Sebastian -- Sebastian Moeller telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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-localGI using compiled matlab - solved
by Bill Taylor 29 Aug '11

29 Aug '11

We here at the University of Wisconsin, Madison are constrained to run only compiled Matlab on our clusters. We have a number of groups that use freesurfer on I have just completed creating some workflows to do longitudinal, -localGI and a basic processing using autorecon1,2 and three. These run in our center on execute nodes not requiring a license since they use the compiled version and a runtime. For the -localGI: Besides the basics of running a compiled matlab in terms of setting up the environment right, I had to change mris_compute_lgi and some input mappings in some of the freesurfer matlab toolbox. My changes had all the args coming into matlab as strings and I had to find the trouble ones(10 or so) and convert them to the proper expected type . This allows thousands of jobs to be analyzed at once on our cluster. Anyone willing to take charge of these changes back at Harvard. It would be great to have this variation available to others. -- Bill Taylor 608-263-2656 (cell 608-219-4430) Center for High Throughput Computing(CHTC) Condor project Computer Sciences University of Wisconsin, Madison

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Freesurfer August 2011