Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

converting .nii.gz label to .label for FS
by kwa1＠rice.edu 31 May '11

31 May '11

Hello, I've derived a .nii.gz atlas-based volume for a specific part of the cortical surface. I've binarized the volume and now I want to convert the file to a .label file that I can use to identify particular vertices in native FS space for that same subject. This is what I have tried so far: mri_vol2surf --src mask.nii.gz --srcreg /tmp/reg.dat --surf pial --projfrac 0.5 --hemi lh --out mask.surf.nii.gz mri_cor2label --i mask.surf.nii.gz --id 1 --l mask.label --surf SUBJ1 lh pial However when I overlayed the .label onto SUBJ1 the vertices did not match up and was completely off the region of interest on the cortical surface. Does anyone know how to fix this or how to proceed with conversion differently? Thank you very much, Kareem

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Error: Bad CPU type in executable.
by ANN40＠pitt.edu 31 May '11

31 May '11

Hi, I recently downloaded and installed FreeSurfer on my Mac and I am having some trouble. I followed the instructions and the installation menu said that everything had been installed correctly. However, when I tried testing if everything worked using the commands provided on the FreesurferWiki website, I got the error "Bad CPU type in executable". Do you know what could be causing this problem? Thank you, Ashley Nielsen

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Tracula bedp error
by Shanqing Cai 31 May '11

31 May '11

Hi, I am running Tracula on the MIT BCS cluster. The first step "-prep" finished without error. However, during the second step "-bedp" I received the following error messages. ba3:~/STUT/tracula> trac-all -bedp -c ~/STUT/tracula/tracula.cfg INFO: SUBJECTS_DIR is /users/cais/STUT/FSDATA INFO: Diffusion root is /users/cais/STUT/tracula Actual FREESURFER_HOME /software/Freesurfer/5.1.0 ln -sf /users/cais/STUT/tracula/S01/dlabel/diff/anat_brain_mask.bbr.nii.gz /users/cais/STUT/tracula/S01/dmri/nodif_brain_mask.nii.gz ln -sf /users/cais/STUT/tracula/S01/dmri/dwi.nii.gz /users/cais/STUT/tracula/S01/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /users/cais/STUT/tracula/S01/dmri subjectdir is /users/cais/STUT/tracula/S01/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: SGE: unexpected operator [: 314: SGE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator Queuing parallel processing stage [: 223: SGE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x67: unexpected operator Queuing post processing stage [: 223: SGE: unexpected operator [: 314: SGE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator It seems that there are errors related to SGE configurations. Anyone has any suggestions w.r.t. how to solve this problem? Thanks! Best regards, Shanqing

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mgh conversion
by Gabriel Go.Es. 31 May '11

31 May '11

Dear freesurfers I want to convert an .mgh image to NIfTY format, but even when the conversion using "mri_convert" seems to be ok, when I try to open the nii, an error message appears "image doesn't appear to be a valid 2D or 3D image", there is any other way to convert an mgh image to nii? In other cases when I tryed to convert other mgh's cointaining clusters extracted with matlab but saved with the same matrix header as "sig.mgh", FS says that nrows in volume exceeds 32768, and does not make the conversion? Any ideas? Thanks in advanced, Gabriel.

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problem creating contrast matrix for f test
by Pablo Polosecki 31 May '11

31 May '11

Dear list: I am analyzing functional data using FSFAST. I have 7 conditions in a blocked design and I would like to run an F-test using the following contrast matrix: [ -0.5000 0 0.5000 0 -0.5000 0.5000 0; 0 -1.0000 0 1.0000 0 0 0] For this I am manually creating a matlab file with the contrast matrix in the “mystudy” folder. (Is there a way of having FSFAST create the matrix for me using mkanalysis-sess ?) I am attaching the matlab m-file with the matrix, which contains this matrix as the ContrastMtx_0 variable. In the matlab file, I set sumconds to 0. I am unsure as what to waht the WCond matrix should be in the matlab file. I am making it equal to the ContrastMtx_0, but this might be wrong. Afterwards I run the analysis using selxavg3-sess, from matlab using (“rois” is the name of the analysis): unix([FS_HOME '/fsfast/bin/selxavg3-sess -analysis rois -sf sf -df df -float -overwrite -monly tmp_gen_rois.m']); tmp_gen_rois; Within text output, I get the following: Computing contrast matrices …(some stuff regarding other contrast matrices)… 3 main_faces J= 3 eff = 287636151.3 vrf = 862908453.9536 vrfffx = 852078020.3613 r = 1.01 This last line says that for main_faces J=3, but my contrast matrix has 2 rows (I understand J is the number of lines in the matrix)! Could someone point out what I am doing wrong here? Thank you very much Pablo

2 1

fsaverage error with recon-all
by Ayaz, Muhammad 31 May '11

31 May '11

Dear All, I ran recon-all using single MPRAGE data set. Processing exited with an error pasted below indicating there is not fsaverage. Thanks Ayaz #@# BA Labels lh Fri May 27 21:47:56 CDT 2011 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... ln -s /usr/local/freesurfer/subjects/fsaverage /usr/local/subjects/fsaverage ln: creating symbolic link `/usr/local/subjects/fsaverage': Permission denied mri_label2label --srcsubject fsaverage --srclabel /usr/local/subjects/fsaverage/label/lh.BA1.label --trgsubject 3t3999_3_1_MPRAGE --trglabel ./lh.BA1.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /usr/local/subjects/fsaverage/label/lh.BA1.label srclabel = /usr/local/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = 3t3999_3_1_MPRAGE trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /usr/local/subjects/fsaverage/label/lh.BA1.label Linux MRI-WorkStation 2.6.32-31-generic #61-Ubuntu SMP Fri Apr 8 18:25:51 UTC 2011 x86_64 GNU/Linux recon-all -s 3t3999_3_1_MPRAGE exited with ERRORS at Fri May 27 21:47:56 CDT 2011 The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

3 3

PhD position in functional neuroimaging
by Michels Lars 31 May '11

31 May '11

PhD position in functional neuroimaging in patients with neurogenic and non-neurogenic lower urinary tract dysfunction Applications are invited for a doctoral research position in the human neuroimaging project "The bladder and the brain - supraspinal control of impaired lower urinary tract function in patients with neurogenic and non-neurogenic bladder dysfunction", funded by the Swiss National Science Foundation (SNF, 32003B_135774/1). Starting September 2011, we will investigate supraspinal lower urinary tract (LUT) control in patients with neurogenic (i.e. multiple sclerosis) and non-neurogenic bladder dysfunction. Patients with non-neurogenic LUT dysfunction will be investigated before and after therapy for their LUT dysfunction. The neuroimaging investigations will consist of a combination of advanced functional (functional MRI for resting state functional connectivity) and structural (diffusion tensor imaging (DTI) and voxel-based morphometry (VBM)) brain imaging methods. The candidate has the chance to participate in an innovative and multidisciplinary research project that is based on the long-standing successful collaboration and renowned scientific groundwork of the Institute of Neuroradiology at the University Hospital Zurich and the Neuro-Urology Research Group at the Balgrist University Hospital. The candidate should hold a Master's degree in neuroimaging, neuroscience, neurobiology, neuropsychology, neurophysiology, physics, or a related field. Fluency in spoken and written English and the ability to work within a multidisciplinary team are essential. Good oral German language skills are not mandatory but are advantageous. Experience with human MRI, or other brain imaging methods is an advantage. Familiarity with analysis software, such as SPM/Matlab or FSL, and experience with programming languages and statistical analysis is a great plus. Salaries are in accordance with the Swiss National Science Foundation (starting at around 40'000 CHF p.a.). For further information about the project please contact Dr. Lars Michels (lars.michels(a)kispi.uzh.ch) Your application includes your CV with a cover letter including a description of your motivation and research interests, a copy of your academic degree(s), and two academic referees to the address below. Reviews of applications will begin on 1 June 2011 and will continue until the position is filled. Dr. Lars Michels Department of Neuroradiology University Hospital Zurich Sternwartstr. 6 Zürich 8091 Switzerland

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going between scanner space and freesurfer space
by Trina Kok 30 May '11

30 May '11

Hi All, We would like to obtain a matrix to go from the orig.mgz/001.mgz space to freesufer space (i.e. that of T1.mgz, brain.mgz etc). I'm not sure which combination of vox2ras and ras2vox of the 2 volumes to extract to be able to obtain say for example, matrix T below. [orig.mgz (appended with ones for extra dimension] = T * [T1.mgz (appended with ones for extra dimension]; On a separate note, I'm using the affine function shown here in the below link to test out the transformations. The function does the interpolation by trilinear interpolation, and does rotation, shearing, scaling etc first, and the translation as a last step. http://www.mathworks.com/matlabcentral/fileexchange/21080. Is this the same or almost the same procedure used in going from scanner space to freesurfer space? Thanks a lot! Cheers, Trina

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cluster and FS new-version adaptation
by Alexandru Hanganu 30 May '11

30 May '11

Dear Freesurfer experts, 1) How many simultaneous processing can be done on a cluster ? I did 20 analysis at the same time, and it worked. They all finished without error. (didn't find this question on the list) 2) In order to adapt the previous subject analysing to the new FS-5.1, must I use the tags: -clean-bm -clean-tal (i.e. recon-all -subjid SUBJ -autorecon1 -clean-tal -clean-bm) Seems that the new analysis doesn't overwrite the previous data. Thank you in advance, Alex. * *

2 1

Source code access
by Trina Kok 30 May '11

30 May '11

Hi all, I have an nmr center account and tried to checkout the FREESURFER source code. I logged in to door.nmr.mgh.harvard.edu via x-win, and then copied the following commands setenv CVSROOT /autofs/space/repo_001/dev cvs checkout -P dev but the following error appeared. I was wondering how should I go about looking at the code? Thanks! cvs checkout: failed to create lock directory for `/autofs/space/repo_001/dev/CVSROOT' (/autofs/space/repo_001/dev/CVSROOT/#cvs.history.lock): Permission denied cvs checkout: failed to obtain history lock in repository `/autofs/space/repo_001/dev' cvs checkout: Updating dev cvs checkout: failed to create lock directory for `/autofs/space/repo_001/dev/dev' (/autofs/space/repo_001/dev/dev/#cvs.lock): Permission denied cvs checkout: failed to obtain dir lock in repository `/autofs/space/repo_001/dev/dev' cvs [checkout aborted]: read lock failed - giving up

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