Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

watershed error
by Janosch Linkersdörfer 16 Jul '14

16 Jul '14

Hi all, recon-all runs smoothly for all my subjects but one. It throws the error "mri_watershed Error: indices out of bounds" and finishes (see https://www.dropbox.com/s/4del0uy8g1qw5az/recon-all.log) The image quality does not seem to be different... The error has been discussed on the list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021896.…) but I don't know where in the brain and in which image space I should add control points or what else I can do to prevent this from happening. Thanks for your help, Janosch

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recon-all exits after mri_nu_correct
by ISAAC PEDISICH 15 Jul '14

15 Jul '14

Hi All, I'm trying to reconstruct surfaces using recon-all. Though many of the subjects have succeeded, a few are failing at the mri_nu_correct stage. The error file (posted below) provides little detail as to why the error is occurring. Even if it is not fixable, it would be nice to know what caused this error. I can provide data if requested. Thank you for your help, Isaac The following is the contents of the reocn-all.error file: ------------------------------ SUBJECT UP044 DATE Thu Jun 26 11:19:36 EDT 2014 USER analy HOST rhino.psych.upenn.edu PROCESSOR x86_64 OS Linux Linux rhino.psych.upenn.edu 2.6.18-371.4.1.el5 #1 SMP Thu Jan 30 06:08:24 EST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/global/freesurfer/bin/recon-all PWD /data3/eeg/freesurfer/subjects/UP044/mri CMD mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

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sulcal depth
by Aleksandar Ristic 15 Jul '14

15 Jul '14

Hi Freesurfer experts, I did thickness group analysis in pts and healthy subject groups in qdec (age corrected( and got thicker cortex in left insula and thinner precentral gyrus bilaterally that survived FDR 0.01 Surface area and curvature analysis found no difference. However, sulcal depth analysis reveled striking difference (positive) in bilateral insula (survived FDR 0.001). As this finding can attribute significantly to understanding of the background of investgated disorder, I kindly ask for representative references covering sulcal depth method (as the variability of the folding patterns is still largely not understood, and different methods have been employed already to best of my knowledge). Second, do I have to correct sulcal depth for age? thanks, Alex Aleksandar J. Ristić, MD, PhD Epilepsy Center Neurology Clinic, Clinical Center of Serbia University of Belgrade, Belgrade - Serbia --- avast! antivirus zaštita je aktivna stoga ova e-pošta nema virusa i zlonamjernih programa. http://www.avast.com

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Is there any saving a brain from this type of error?
by Jonathan Holt 15 Jul '14

15 Jul '14

Attached is an image of wm.mgz after a routine recon-all...

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Re: [Freesurfer] Fw: Re: Problem with uploading Cluster Simulation data
by Douglas N Greve 15 Jul '14

15 Jul '14

You have to load a surface and then load the overlay on top of that. See the freeview tutorial doug ps. Please post to the list! On 07/15/2014 09:03 AM, carina(a)van-vlodrop.de wrote: > I have opened freeview with the commands 'freesurfer' and 'freeview'. > I thought that I could upload the data directly in freeview. Or which > command do I need? > *Gesendet:* Montag, 14. Juli 2014 um 19:38 Uhr > *Von:* "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > *An:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de>, > "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> > *Betreff:* Re: Fw: Aw: Re: [Freesurfer] Problem with uploading Cluster > Simulation data > > what is your command line? Or otherwise, how are you visualizing it? > > > > On 07/14/2014 08:09 AM, carina(a)van-vlodrop.de wrote: > > *Gesendet:* Sonntag, 06. Juli 2014 um 22:48 Uhr > > *Von:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de> > > *An:* "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> > > *Betreff:* Aw: Re: [Freesurfer] Fw: Problem with uploading Cluster > > Simulation data > > Hi Doug, > > I have already uploaded a text file of my corrected results from the > > Monte Carlo Cluster Simulation which reports 15 Clusters (attached > > picture). > > There is another file ending with .mgh and the tutorial identifies it > > to be the overlay (clusterwise corrected map) which I can upload in > > freeview. > > In freeview there are the alternatives of uploading a surface or a > > volume. If I upload the file ending with .mgh as a volume I just > > recieve a black image with a few numbers on the coordinate plane > > (attached picture). There is no brain visible. > > Is it correct to upload the overlay (file ending with .mgh) as a > > volume or how should I proceed? Do I have to upload a template first > > and which is the right template? > > Thank you so much. > > Yours sincerely, > > Carina > > *Gesendet:* Montag, 16. Juni 2014 um 12:45 Uhr > > *Von:* "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> > > *An:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de>, "free surfer" > > <freesurfer(a)nmr.mgh.harvard.edu> > > *Betreff:* Re: [Freesurfer] Fw: Problem with uploading Cluster > > Simulation data > > > > You should be able to view the map results in freeview just as you > > would any other map. > > doug > > > > > > > > > > > > On 6/12/14 12:19 PM, carina(a)van-vlodrop.de wrote: > > > > *Gesendet:* Dienstag, 10. Juni 2014 um 11:18 Uhr > > *Von:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de> > > *An:* freesurfer(a)nmr.mgh.harvard.edu > > *Betreff:* Problem with uploading Cluster Simulation data > > Dear freesurfer experts, > > we are conducting cortical-thickness analysis using > > freesurfer-4.4.0 and the final analysis with qdec. I have a > > question concerning the Clusterwise Correction for Multiple > > Comparison. > > Is it correct that I have to visualize the results of the Monte > > Carlo Simulation in freeview? > > Do I have to upload a special model in freeview before uploading > > the Cluster Simulation data? > > Yours sincerely, > > Carina > > > > > > _______________________________________________ Freesurfer mailing > > list Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Temporal lobe reconstruction problem
by james pardon 15 Jul '14

15 Jul '14

Hi all, On a few subjects with a specific pathology (MS) I cannot easily reconstruct temporal lobes. I think this issue comes up quite regularly on the mailing list, and I have tried to trouble shoot using control points, WM edits, even getting back to orig/001.mgz to correct areas that may seem the culprit for breaking surface reconstruction. Some subjects have gone through 7-8 runs of recon-all with different edits but still the problem persists in a few subjects in my study. I have also tried to use -mprage and -3T flags along the way to allow more liberal control point growing, despite an improvement in my results some of subjects still have very bad surface constructions. I have attached two snapshots to this email and I am happy to upload the complete subject folder if you need to take a look at them. As far as the SNR is concerned, I have designed my study based on recommended Freesurfer parameters a couple of years ago on 3T Siemens Trio with 32-channel receiver coil. A huge thank you for your previous helps, and thanks in advance for helping me with this new issue. James

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Updated process v. files excel sheet?
by Makaretz, Sara Johanna 15 Jul '14

15 Jul '14

Hi all, I like the excel presentation of the recon-all process/files table for Freesurfer 3.0.5 found here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps Is there an updated document for a more recent version? (I am using 5.3.0) Also, are 5.2 and 5.3 similar enough to reference the 5.2 stable table for file order/rerunning steps? (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.2) Thank you! Sara

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Making Substancia Nigra label
by Shantanu Ghosh 15 Jul '14

15 Jul '14

Dear Freesurfer experts, I have a set of T2w Dicoms from Parkinson's patients and Control subjects. I want to extract and visualize the Substancia Nigra regions of each of these brains. Can you please suggest a way to do this (command line instructions would be great)? Thanks in advance. Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg

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Cerebellar Vermis
by Sarosh, Cyrus 15 Jul '14

15 Jul '14

We are interested in using the Cerebellar vermis for an analysis with our PET data. Is the cerebellar vermis segmented during the FreeSurfer pipeline analysis? If it is, which file is it located in or how can I export a nifti file containing this segmentation? Thanks, Cyrus Sarosh [Description: Description: Description: Description: Description: Description: Description: cid:image002.png@01CC3BB7.F8D9A990] Research Technician Senior Department of Radiology Functional Neuroimaging, Cognitive and Mobility Laboratory ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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(no subject)
by Hugh Pemberton 15 Jul '14

15 Jul '14

Hi everyone, I'm getting the follow error and it's jus started happening after updating Xquartz.. any ideas what I can do? Also, i dont have a .debug_tkmedit file, when tkmedit was running normally the first line would say could not create debug file. Many thanks, Hugh ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting...

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Freesurfer July 2014