Freesurfer

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30096 discussions

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.

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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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T or Z values in QDEC
by Kelly, Philip 17 May '13

17 May '13

Dear Freesurfer list members, Within QDEC I have found a number of clusters that show significantly different cortical thickness and local gyrification between two groups. The cluster summary exhibits the p value, coordinates and other information regarding the cluster, however I wanted to report the t or z values and was unsure in finding or computing this from QDEC. The p-value must be computed from one of these scores but I could not find it to be reported in any of the output. Searching on the mailing list and tutorials, I could not find an easy solution to this. Thanks for your time and I look forward to hearing back. All the best, Philip Kelly

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incomplete forceps
by Roschinski, Benjamin 17 May '13

17 May '13

Dear Freesurfer experts, we have a problem with the forceps. After the first trac-all we had a forcpes minor with a really unusually structure so we tried to fix it with an rerun of the trac-all. The result was a forceps minor with a third thigh in the sagittal axis. We did a second rerun and now the forceps minor normalized. Our problem is that we don´t know if we should do more trac-all reruns by other patients with difficult tracula or how we should interpret this result. Do you have any ideas to solve this? The second problem is that we have many many tracula results with incomplete forcepes minor or major. We know that the forcepes are the most difficult tracts because of the curvature but do you have some ideas to fix that problem? Kind regards Benjamin

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recon-all error: Correcting Defect 2
by Sudhin A. Shah 17 May '13

17 May '13

Hi, I got the following error: CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Thanks, S

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conversion from ascii to surface
by Tina Jeon 17 May '13

17 May '13

Dear Doug, Nick, and all, I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer. Do you have any suggestions for how I could do the conversion? Thank you in advance! All the best Tina Jeon PhD Candidate UT Southwestern Medical Center '14 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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