Freesurfer

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30090 discussions

Perirhinal Cortex
by Rob Tennyson 19 May '13

19 May '13

Hi All, I want to extract the volume of the perirhinal cortex from a group of subjects processed on fs5.1. Is it possible to run the balabel on these subjects in 5.2 without running the full recon-all for them? If it is possible, is it advisable not to run the full recon-all on 5.2 with them first? Thanks! Rob

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any way to parallelize Tracula?
by Hoptman, Matthew 19 May '13

19 May '13

Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ________________________________ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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recurring spike on inflated surface
by Michael Spilka 18 May '13

18 May '13

Hello, I am fairly new to freesurfer so I hope that my question makes sense: I have been inspecting the inflated surfaces of my reconstructed data in order to detect any issues with white matter segmentation. I have noticed a recurring issue for most of my subjects: the presence of a "spike" on the left hemisphere medial surface (see attached jpeg for an example). The spike appears in roughly the same location for every subject. Has anyone encountered this type of recurring segmentation error? Is there an easier fix than manually editing the segmentation for each subject? Thanks!! Michael

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data analysis
by Roschinski, Benjamin 18 May '13

18 May '13

Dear Freesurfer users and experts, for the first time we used TRACULA 5.1.0 to visualize the tracts of our test persons and now we did the update to TRACULA 5.2.0. We did a rerun of the trac-all logarithm for all test persons in order to achieve better TRACULA results. At one point we had patient with good TRACULA outputs (all tracts are complete) by using 5.1.0 but the same person had a worse TRACULA output by using 5.2.0. There have also bin test persons that recieve good tract result with TRACULA 5.2.0. than with 5.1.0. Now we would like to know if we can use TRACULA 5.1.0 data for one person with good tracts and for another person TRACULA 5.2.0 data with good tracts as well but both with worse tracts when using the different TRACULA version? Summarizing we would like to know if we can mix the data analysis with data from TRACULA 5.1.0 and 5.2.0? Kind regards Benjamin PS: I have sent you another message on the sixth of May. Can you help me with this problem as well?

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QDEC and Hippocampal subfields
by Marcos Martins da Silva 17 May '13

17 May '13

Hi, freesurfers I have two questions: 1- Is there a way to use QDEC to analyze data from hippocampal subfields created by recon-all -s subj -hippo-subfields? That is, I know I can manually put data from posterior* files when making the FSGD file but it would be great if I could import it like I do from aseg.stats. 2- Assuming all data from my subjects are already are already in the FSGD, I understand I can select cortical thickness or volume as dependent variable and inspect the correlations between cortical thickness and age, for example. But I could not find how to define a hippocampal subfield volume as a dependent variable. Is that possible? This way I could display correlations between a subfield volume and age or gender. Thank you, Marcos

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FW: Tracula problem
by Hoptman, Matthew 17 May '13

17 May '13

Hi Anastasia, I'm just forwarding a modified version of the email I'd sent you earlier to the list so everyone can see it. I solved this particular problem in a new dmrirc, but it seemed that I had to modify trac-preproc to remove the ${dcmroot} in front of: infile, b0mfile and b0pfile: diff bin/trac-preproc bin/trac-preproc.orig < if ($#dcmroot > 0) set infile = $infile --- > if ($#dcmroot > 0) set infile = $dcmroot/$infile 259c259 < endif --- > endif 296c296 < set dcmfile = $b0mfile --- > set dcmfile = $dcmroot/$b0mfile 311c311 < set dcmfile = $b0pfile --- > set dcmfile = $dcmroot/$b0pfile But now it doesn't seem to loop through the subjects, so I'm doing them one at a time (painful). Also, if, as in my other question, I try to run this as a cluster job, I don't know how I can substitute a new subject into subjlist. I have 64 subjects and would like to do trac-all -prep -c dmri on all of them simultaneously. I have used bedpostx in SGE, but there you can just write loop to get it to go through your subjects. If I could make the subject variable external to dmrirc, I could do easily script the trac-all job to run in SGE, but I can't fiugre out how to pass it to the trac-all command. Is there any way to pass the subject number directly to the command? Does this make sense? Matt -----Original Message----- From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 12:31 PM To: Hoptman, Matthew Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem Hi Matt - Can you source try this on the command line: source dmrirc_53beta echo $b0mlist echo $b0plist Are these filenames correct, do these files exist? This is how you define them in your configuration file: set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head -1`) set b0plist = (`ls ${SUBJECTS_DIR}/${subjlist}/fphas/ | sort -n | head -1`) Thanks, a.y On Wed, 15 May 2013, Hoptman, Matthew wrote: > > Hi all, > > > > I’m having a problem with tracula. I’m trying to run in version 5.3 beta (is that > version very different from the newer 5.3?). If I run > > trac-preproc -c dmrirc –prep, > > > I get: > > mri_convert /home/hoptman/freesurfer/subjects/c159032/ > /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz > > mri_convert /home/hoptman/freesurfer/subjects/c159032/ > /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz > > corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info > > > > I don’t know why it would look for COR-.info in the subjects’ root directory. I’m > attaching my dmrirc file in case that helps. > > > > Thanks, > Matt > > Matthew J. Hoptman, PhD > Research Scientist V > Nathan S. Kline Institute for Psychiatric Research > > Research Associate Professor in Psychiatry > NYU School of Medicine > > > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. > It may contain confidential information which is legally privileged or otherwise > protected by law. If you received this > e-mail in error or from someone who was not authorized to send it to you, you are > strictly prohibited from reviewing, using, disseminating, distributing or copying > the e-mail. > > PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE > FROM YOUR SYSTEM. Thank you for your cooperation. > > > > __________________________________________________________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. > It may contain confidential information which is legally privilegedor otherwise > protected by law. If you received this e-mail in error or from someone who is not > authorized to send it to you, you are strictly prohibited from reviewing, using, > disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF > THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for > your cooperation. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. > It may contain confidential information which is legally privileged or otherwise > protected by law. If you received this e-mail in error or from someone who is not > authorized to send it to you, you are strictly prohibited from reviewing, using, > disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF > THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for > your cooperation. > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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Tracula problem
by Hoptman, Matthew 17 May '13

17 May '13

Hi all, I'm having a problem with tracula. I'm trying to run in version 5.3 beta (is that version very different from the newer 5.3?). If I run trac-preproc -c dmrirc -prep, I get: mri_convert /home/hoptman/freesurfer/subjects/c159032/ /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz mri_convert /home/hoptman/freesurfer/subjects/c159032/ /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info I don't know why it would look for COR-.info in the subjects' root directory. I'm attaching my dmrirc file in case that helps. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ________________________________ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

2 2

weighted DTI metrics for each section
by celine＠nmr.mgh.harvard.edu 17 May '13

17 May '13

Hi Freesurfer team I would have a question about the Tracula output. If I understand it correctly, the output of the file: pathstats.byvoxel.txt can give us a mean average of DTI metrics at each section of the tract. Is there a way to get the weighted_FA, AD RD and MD at each section? Thanks for your help. Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

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Freesurfer MAC installation
by Flavia Niccolini 17 May '13

17 May '13

Hi I am having trouble with the license file. I created in Freesurfer a file named ".license" but I cannot open this and copy the license. where and how should I put the 3 lines license? I tried to test my freesurfer installation with Bert but I got as answer "command non found". Please help BW Flavia

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tracula error
by Skyler Gabriel Shollenbarger 17 May '13

17 May '13

Hi all, We ran tracula prep stage and it exited with errors: 'Selected streamline has fewer than 5 points'. We have attached the log and error files if needed. Thank you in advance! Skyler -- Skyler G. Shollenbarger Graduate Student - UWM Brain Lab Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee

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