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30132 discussions

mri_cvs_register can not find
by Martin Kavec 04 Nov '11

04 Nov '11

Hi all, I am trying to run mri_cvs_register but for some reasons it always terminates with: ERROR: Can not find or read $SUBJECTS_DIR/MY_SUBJECTS/cvs/combined_tocvs_avg35__elreg_aseg.m3z My command is as follows: mri_cvs_register --mov MY_SUBJECT Indeed the file is not there, but another one with the exactly the same name, but different suffix .tm3d is there. Anybody encountered similar problem? Any idea what can be wrong? Thanks in advance, Martin

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How to specify -gcut for Freesurfer 5.1 release
by Vy Dinh 03 Nov '11

03 Nov '11

Dear Experts, I've read that the latest Freesurfer release, v5.1, allows one to rerun the skullstripping step to remove extra dura. This would be a godsend for us since most pial surface corrections involve removing the dura. However, we have been using v5.0, which does not have this feature. It also appears that mri_gcut, the v5.0 equivalent of -gcut, is run by default in v5.0. Could someone please confirm this? I'd really appreciate it if there is a way to remove the extra dura automatically after running recon-all. Since we preprocessed our subjects using v5.0, we have not used v5.1 at all, unless it is more beneficial to start editing using v5.1. Thanks in advance, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu>

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converting "annotation values" to "label codes"
by David Grayson 03 Nov '11

03 Nov '11

Hi, I have converted a custom-made annotation file to a volume, and now I am trying to find a table with the labels and their corresponding label codes (index values which are created when the annotation file is converted to a volume). I only have the “annotation values” or color codes for each region, which I found with the read_annotation() function in matlab. The online wiki states that this color code then has to be used to look up the label code, but it’s unclear to me how to do this. Is there be a table somewhere so that I can cross-reference the color codes to the label codes? Thank you, David

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missing clusters in cwp simulation cluster summary?
by Martina Ly 03 Nov '11

03 Nov '11

Hi freesurfers, According to the page on group analysis( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) the cluster summary contains ALL clusters, regardless of their significance. However, a paracentral cluster (see figure attached) had a uncorrected p value of 10^-6 but doesn't show up in mz-c.sig.cluster.summary even after I lowered the cwpvalthresh to 0.1 in a cwp simulation. Any advice or suggestions would be greatly appreciated. Many thanks, Martina

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Monte Carlo Simulation algoritm for multiple comparisons correction
by Alexander Ivanov 03 Nov '11

03 Nov '11

*Dear Freesurfer Users and Developers, * Could you please help me to clarify the key steps implemented into the Monte Carlo approach for multiple comparisons correction? As far as I understood, it consists of running many permutations for fitting the measurements of different ROI sizes, which are being selected randomly according to predefined p-value. The process stops when optimal cluster is found and as a result we have the clusters of difference with clusterwise p-value and 90% C.I.... Am I wrong? Thank you very much beforehand... Regards, Alexander Ivanov

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right orbitofrontal cortex uncorrect segmentation
by _andreia_＠sapo.pt 03 Nov '11

03 Nov '11

Hi all, I'm getting this problem is many subjects (see attached files). As you can see the wm is not being properly classified. Adding control points or editing the wm file usually works, however I would like to know if this is usual and if there is a way to avoid the need for always manually correct this defect. Andreia

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Tracula Question, step 2
by Shannon Buckley 02 Nov '11

02 Nov '11

Hi Anastasia, I am trying to run Tracula for the first time in our lab and I'm getting errors during step 2 that seem to involve how the program wants to be launched via grid. I've attached the configuration file I'm using and the error message is below... _____ $trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh Using Freesurfer version 5.1. Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/ Sessions Directory is /home/vhasfcbuckls/sessions INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1 ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_m ask.bbr.nii.gz /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.ni i.gz ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/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 /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri subjectdir is /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue "short.q". Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue "long.q". Exiting. Queuing post processing stage Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue "long.q". Exiting. _____ Although we DO have a grid, I am trying to test the program for feasibility purposes, just on my own system's terminal, since we aren't sure how results will look with our specific data set (3.0 Tesla Siemens, 64 directional DWI @ b=1000, with 1 b0 image). We are very interested in performing tractography in T1-space. I am open to running this over the grid, if that's really the best way to do it, but the problem is that I don't see anywhere to specify the name of the queue that should be used for launching the program. Can you please tell me how to launch this without using the so-called long.q and short.q? We typically launch jobs to our grid using our "bash.linux.q", but I haven't been able to locate a place in the configuration file, or any switches to use in the cmd line, to specify that this queue should be used. I tried specifically launching Tracula's step 2 onto our bash.linux.q via the cmd line using "qsub", but received the same old error I had been getting. I checked the data independently using "bedpostx_preproc.sh", and it appears that all the required data are set up properly. As far as I can tell, the only issue we have is this inability to use the long.q and short.q. What do you think? I've cc'd our IT specialist, Henry Mensch, who oversees our grid system in case you need someone to chime-in with any specific information about how our Linux systems are set-up. Thanks very much for your time, Shannon T. Buckley SRA III - Supervisor CIND, UCSF 4150 Clement St. (114M) San Francisco, CA 94121 Phone: (415) 221-4810 x4251 Fax: (415) 386-3954

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concerns about symbolic links during processing
by Vy Dinh 02 Nov '11

02 Nov '11

Dear experts, We have recently encountered processing errors (during recon-all and -autorecon2&3) due to the creation of symbolic links within our SUBJECTS_DIR. Since our data were located on a data mount, the system somehow could not source the linked file. We have addressed this issue by directly copying fsaverage and th *EC_average files directly to our current SUBJECTS_DIR so that the symbolic links did not need to be created. However, this brings to light some another concern. The subjects for our study were processed on a local computer and then copied to the server so that they could be processed on multiple computers. Since we wanted to keep a copy of the "raw" reconned data, we copied these subjects to another directory and proceeded to do manual edits. Are there other symbolic links created within the subjects directories or SUBJECTS_DIR that would become defunct with these copies? I read a post in the Freesurfer forum that the link to fsaverage (and other folders) were only created during recon-all for display purposes. However, when running group analyses, these folders/files will need to be accessed, so does that mean that we would have to change the path info in these links? Would you caution against moving the subject directories after recon-all has been run? Rather than all the steps in run recon-all again, are there specific functions that will recreate these links? Thanks, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu>

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Multiple sclerosis lesions
by Carolina Valencia 02 Nov '11

02 Nov '11

Dear FS users, I would like to use FS to calculate WM hypointensitis (so-called black holes) for patients with multiple sclerosis, but 1. I don't know which stat file I should use to report the volumes, such as total WM, WM hypointensities, etc 2. which editing tool I must use when the lesion is not classified as WM hypointensities by FS? I know that the control points are not used or recommended for WM lesions 3. Can I use other sequences for detecting other classes of lesions present in this disease, such as hyperintense T2 lesions (T2WI) or enhacing lesions on contrast enhaced MR, in order to calculate the volumes of those, or just the T1 (MPRAGE) 4. which literature do you suggest for the post processing of these lesions using FS or perhaps another tool? thanks a lot, Carolina

2 1

propagating labels to gray matter
by David Grayson 02 Nov '11

02 Nov '11

Hi freesurfer experts, I currently have a set of cortical labels that are the result of a high-resolution parcellation of the standard aparc.annot labels (via the ‘connectomemapper’ software). I would like to extract the gray matter ROIs that correspond to these labels, and I understand that this requires a method to ‘propagate’ these labels through the gray matter. I have so far been unsuccessful – ‘mri_label2vol’ seems to only give me that pial or white surfaces, as opposed to the gray matter bodies. Does anyone know how to accomplish this? Thank you very much, David Grayson

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