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30132 discussions

curvature of flattening
by Gabriel Go.Es. 31 May '11

31 May '11

Dear FS experts, I'm making some flattenings of one subject on FS and I'm wondering if it is possible to see the ?h.curv or the ?h.sulc on grayscale and not in red-green nor in the binary gray representations of tksurfer. Regards, Gabriel.

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Full-time Research Assistant position in Clinically-Oriented Cogn itive Neuroscience at Virginia Tech
by John Richey 31 May '11

31 May '11

Dear freesurfer users, The following advertisement is for a full-time research assistantship in cognitive neuroscience in the Department of Psychology at Virginia Tech. Please feel free to distribute to interested parties. **Full-Time Lab/Research Assistant Position: Social-Clinical-Affective Neuroscience Lab Description of Position & Duties: A full-time R.A. position is available in the lab of Dr. John Richey in the Department of Psychology at Virginia Tech. The Assistant will be involved in implementing and organizing studies that investigate brain function and structure in the context of autism and affective disorders. The central research program seeks to investigate and quantify in vivo the the relation between particular cortical regions and social-cognitive dysfunction across a range of pathological states. Ultimately, we aim to assess the impact of neurocognitive intervention on cortical function and behavioral/cognitive outcomes in patients. To investigate this, the laboratory utilizes several neuroimaging modalities, including functional magnetic resonance imaging (fMRI), high-resolution structural MRI and diffusion tensor imaging (DTI). The position involves data acquisition in human research subjects, data analysis and administrative tasks. It is expected that the candidate will be able to work collaboratively with an interdisciplinary group of clinicians, psychologists and cognitive neuroscientists to accomplish our research objectives.This is an excellent position for someone wishing to enter graduate or medical school. The start date is negotiable, but would be no earlier than August 1st 2011, and ideally no later than October 1st 2011. A one-year commitment is expected. Requirements: 1) Bachelor's degree in psychology, neuroscience, biomedical engineering, computer science or related field. 2) Strong organizational skills, including ability to prioritize tasks and make decisions independently. 3) Strong interpersonal skills and ability to work with patients. Although not required, experience in the technical aspects of fMRI, including Unix/Linux shell scripting and basic knowledge of common statistical software platforms (MATLAB, freesurfer, FSL) is desirable. The ideal candidate will also have a strong background in statistics, biology and/or neuroscience and a demonstrated interest in research Any interested candidates should provide a cover letter, a resume and the names and contact information of 2-3 references to Dr. John Richey (richey(a)vt.edu) Candidates are also welcome to contact with any questions about the position.

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Appropriate positive control to for overall quality?
by Joakim Vinberg 31 May '11

31 May '11

Hi everybody, I have been analyzing a dataset that has produced some unusual results. Does anybody have any suggestions for a general positive control to ensure data and segmentation quality? I am thinking along the lines of comparing the results of measurements with age to Salat, 2004: Thinning of the Cerebral Cortex in Aging, or perhaps sex differences (both of these measurements would be relatively independent of my investigations). Thanks in advance! Joakim

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poor wm segmentation
by kwa1＠rice.edu 31 May '11

31 May '11

Hello all, I have a subject for whom I have been trying to edit the wm segmentation. This last time was the fifth time I have run the subject through autorecon2 and I am still achieving quite poor wm segmentation and pial tracings. To try and solve the problem I keep drawing in more of where the wm should be and removing it where it should not (on the aux surface). I have also tried adding control points but to no avail. Does anyone have a solution for how to proceed? This subject has no abnormalities that would otherwise limit the accuracy of the segmentation and I see no reason for it not to work. The scan also has decent contrast (same as all the other subjects who had great segmentation in FS). Thank you in advance, Kareem

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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

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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.

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