Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Talairach Conversion
by Ishan Patel 14 Oct '15

14 Oct '15

Hello, I wanted to use the function: mri_label2label to convert my label file into talairach space. This is the output that I am getting. On the mri_label2label information page, it says to use 'talairach' as the target subject which is what I did, but it cannot find 'talairach'. Does anyone have experience with this? [image: Inline image 1]

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Re: [Freesurfer] Segmentation fault using mri_label2vol
by Syeda Maryam 14 Oct '15

14 Oct '15

So for some reason my mail with the attachments won't get delivered...the message size exceeds the limits. I was wondering if the segmentation fault error I'm getting might be do to some problem in the freesurfer version I'm running? Thanks,Syeda On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam <swajiham(a)yahoo.com> wrote: I'm not sure if my last message got delivered or not so I'll resend it. Thanks very much for looking into this so quickly. Sure thing! I've attached the images here. The aseg file opens up with freeview, and the mri_label2vol command works fine on my local machine but when I try to implement it on our server using nipype, it gives me the error I mentioned. Best, Syeda On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam <swajiham(a)yahoo.com> wrote: Thanks very much for looking into this so quickly. Sure thing! I've attached the images here. The aseg file opens up with freeview, and the mri_label2vol command works fine on my local machine but when I try to implement it on our server using nipype, it gives me the error I mentioned. Best,Syeda On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Syeda that commnand doesn't segfault when I try it on another subject here. If you email me the aseg.mgz and the rawavg.mgz I'll take a look cheers Bruce On Wed, 14 Oct 2015, Syeda Maryam wrote: > Hello Freesurfer experts, > > I'm getting a segmentation fault when I use the mri_label2vol command to push aseg labels from freesurfer space to my > subject's original T1 space (using the example given on the freesurfer website). I'm not sure why this is > happening...I've tried changing the parameters countless times but nothing has worked. I also checked my "aseg.mgz" to > make sure it's not corrupted but that isn't the issue either. Any help would be highly appreciated!! Thanks in advance > > mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp > /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz > Number of labels: 0 > Annot File: (null) > Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz > Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz > Registration File: (null) > Fill Threshold: 0 > Label Vox Vol: 1 > ProjType: (null) > ProjTypeId: 0 > ProjStart: 0 > ProjStop: 0 > ProjDelta: 0.1 > Subject: (null) > Hemi: (null) > UseNewASeg2Vol: 1 > DoLabelStatVol 0 > LabelCodeOffset 0 > setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ > Template RAS-to-Vox: -------- > -0.985 0.000 0.000 128.000; > -0.000 -0.000 -0.985 128.000; > -0.000 0.833 -0.000 98.000; > 0.000 0.000 0.000 1.000; > Template Voxel Volume: 1.23773 > nHits Thresh: 0 > Computing registration based on header > RegMat: -------- > 1.000 0.000 0.000 -0.000; > 0.000 1.000 0.000 0.000; > 0.000 0.000 1.000 0.000; > 0.000 0.000 0.000 1.000; > Label RAS-to-Vox: -------- > -0.985 0.000 0.000 128.000; > 0.000 0.000 -0.985 128.000; > 0.000 0.833 0.000 98.000; > 0.000 0.000 0.000 1.000; > ASeg2Vol: Building LUT > Segmentation fault > > > 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.

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Segmentation fault using mri_label2vol
by Syeda Maryam 14 Oct '15

14 Oct '15

Hello Freesurfer experts, I'm getting a segmentation fault when I use the mri_label2vol command to push aseg labels from freesurfer space to my subject's original T1 space (using the example given on the freesurfer website). I'm not sure why this is happening...I've tried changing the parameters countless times but nothing has worked. I also checked my "aseg.mgz" to make sure it's not corrupted but that isn't the issue either. Any help would be highly appreciated!! Thanks in advance mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz Number of labels: 0 Annot File: (null) Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -------- -0.985 0.000 0.000 128.000; -0.000 -0.000 -0.985 128.000; -0.000 0.833 -0.000 98.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1.23773 nHits Thresh: 0 Computing registration based on header RegMat: -------- 1.000 0.000 0.000 -0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -0.985 0.000 0.000 128.000; 0.000 0.000 -0.985 128.000; 0.000 0.833 0.000 98.000; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT Segmentation fault

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Segmentation fault using mri_label2vol
by Syeda Wajiha Maryam 14 Oct '15

14 Oct '15

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pial surface encircling the optical chiasm
by Antonin Skoch 14 Oct '15

14 Oct '15

Dear FreeSurfer experts, during inspection of reconstructions of our data, I found that in many cases the pial (and sometimes also white) surface is extending out of the brain and encircling the optical chiasm. Does this situation has any effect to the results (i.e. cortex parcellation, whole-brain group thickness or local gyrification index analysis), i.e. is it an reconstruction error which should be manually corrected? Or can we safely ignore it? Regards, Antonin Skoch

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Post-doctoral Fellowship in longitudinal image analysis at UCL
by Arman Eshaghi 14 Oct '15

14 Oct '15

Apologies for the spam, we thought this might be of interest for Freesurfer users. A postdoctoral position in longitudinal image analysis is available within the Centre for Medical Image Computing (CMIC) at UCL Department of Computer Sciences, London, UK. We are seeking a highly motivated individual to work within the Progression of Neurological Disease (POND) Group cmic.cs.ucl.ac.uk/pond, led by Prof. Daniel Alexander, on computational-statistical neurological disease progression within the Horizon 2020 EuroPOND project: www.europond.eu. See http://cmic.cs.ucl.ac.uk/pond/vacancies/ for more details and the application procedure. If you have any queries regarding the vacancy or the application process please contact Dr Neil Oxtoby n.oxtoby(a)ucl.ac.uk. ————————————————————————— Arman Eshaghi, MD PhD Student UCL Institute of Neurology Queen Square Multiple Sclerosis Centre 1st Floor, Russell Square House 10-12 Russell Square London WC1B 5EH Tel: (+44) (0) 203 108 7420 UCL extension: 57420 arman.eshaghi.14(a)ucl.ac.uk Website: http://www.homepages.ucl.ac.uk/~skgtaes/

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Problem with recon-all
by Mads Jensen 13 Oct '15

13 Oct '15

Hi, I got a problem with recon-all of T1's. The problem is that the surfaces extent into what is essential noise, see linked images. The problem is reoccurring in all the subjects I have ran so far, so I was wondering if there could be a generic fix or if it will be necessary to fix each recon individually. The sequence is a MP2RAGE recorded from a Siemens Skyra. thanks, mads https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.j… https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.j… https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.j…

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Re: [Freesurfer] mris__label__calc intersect error in longitudinal qcache
by Martin Reuter 13 Oct '15

13 Oct '15

Hi Bhavani, when I run mris_label_calc intersect MPS-007_2mod.long.MPS-007\ rh.cortex.label MPS-\ 007\ lh.cortex.label out.label it goes through and writes the out.label file. I used fs 5.3 for that. Can you please send me the command and input files that fail for you? About your other questions: qdec tables should be stored in <SUBJECS_DIR>/qdec not sure about the other error. can you send the cross qdec table. probably you need a level file for group? Thanks, Martin P.S. Please post questions to the FreeSurfer list. On 10/13/2015 10:56 AM, Selvaraj, Bhavani wrote: > Hi Martin, > Thanks for the reply. Yes those files are available at these locations. > when I run this command for LH > long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR > it runs smoothly > and gave me these results > tksurfer MPS-007 lh pial -overlay /Applications/freesurfer/subjects/MPS-007/surf/lh.long.thickness-avg.fwhm25.mgh > tksurfer MPS-005 lh pial -overlay /Applications/freesurfer/subjects/MPS-005/surf/lh.long.thickness-avg.fwhm25.mgh > > but for the rh only the patients MPS-007 gave me the error MPS-005 worked fine. > How do I fix that? > I am attaching you the cortex label file I don't know how to tell if it is corrupted. > > Also I have two more question where should I store the QDEC data table > Is this where I should make it? > Applications/freesurfer/subjects/qdec/ long.qdec.table.dat > > also when I try to open the table in Qdec I get the following error: > freesurfer% qdec --table ./qdec/cross.qdec.table.dat > > Reading /Applications/freesurfer/tktools/tkUtils.tcl > > Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl > > Loading data table ./qdec/cross.qdec.table.dat... > Number of columns: 13 > fsid column: 1 > Number of factors: 12 > Number of subjects: 2 > ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: Group for subject MPS-007 > > Thanks Martin for your help! > bhavani > > > ________________________________________ > From: Martin Reuter [mreuter(a)nmr.mgh.harvard.edu] > Sent: Friday, October 09, 2015 8:59 PM > To: Selvaraj, Bhavani > Subject: Re: [Freesurfer] mris__label__calc intersect error in longitudinal qcache > > Hi Bhavani, > > Strange, are those files available at those locations? Can you also check permissions. Open the label files to see if they are corrupted. > Best MartinOn Oct 9, 2015 11:31 AM, "Selvaraj, Bhavani" <Bhavani.Selvaraj(a)nationwidechildrens.org> wrote: >> Hi, >> >> when I try running longitudinal analysis for 2 subjects I get the following error (this error >> >> only persists for the right hemisphere-- left hemisphere works fine for this subject). >> >> >> >> mris_label_calc intersect /Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label >> >> >> >> ERROR -11 : mris_label_calc intersect did not work? >> >> I saw a similar question in the archived mail list so I tried running this command by itself and this was the comment >> >> Segmentation fault >> >> I didn’t know how to fix this error? should I run them again?? >> >> >> >> >> >> Qdec table >> >> Fsid fsid-base years >> >> MPS-007_1 MPS-007 3 >> >> MPS-007_2mod MPS-007 4 >> >> MPS-007_3 MPS-007 4 >> >> MPS-005_1 MPS-005 5 >> >> MPS-005_2 MPS-005 6 >> >> MPS-005_3 MPS-005 6 >> >> >> >> >> >> Thanks, >> >> Bhavani > > 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 > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… . 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. -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu

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FSL GUI error message
by Park, Jung Mi 13 Oct '15

13 Oct '15

Hello When I ran FSL GUI on the Martinos center after typing source freesurfer, I received an error message like that custom widget with id loop-button does not return a valid node on the X-window terminal. How can I solve this problem? Thanks Jung Mi I used FSL 5.0.7, FEAT tool v 6.00 for FSL GUI through the brain vision at Martinos center. Next the information I set: feat main script: /bin/cp /tmp/feat_9l88ef.fsf design.fsf /usr/pubsw/packages/fsl/current/bin/feat_model design mkdir .files;cp /usr/pubsw/packages/fsl/current/doc/fsl.css .files;ln -s /usr/pubsw/packages/fsl/current/doc/images .files/images /usr/pubsw/packages/fsl/current/bin/fsl_sub -T 10 -l logs -N feat0_init /usr/pubsw/packages/fsl/current/bin/feat /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/design.fsf -D /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat -I 1 -init 19094 /usr/pubsw/packages/fsl/current/bin/fsl_sub -T 78 -l logs -N feat2_pre -j 19094 /usr/pubsw/packages/fsl/current/bin/feat /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/design.fsf -D /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat -I 1 -prestats Preprocessing:Stage 1 /usr/pubsw/packages/fsl/current/bin/mainfeatreg -F 6.00 -d /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+++++.feat -l /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/logs/feat2_pre -R /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/report_unwarp.html -r /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/report_reg.html -i /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/example_func.nii.gz -n 10 -h /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/fsl_T1 -w 3 -x 90 -s /autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/5.0.7/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 Option -s ( standard image ) selected with argument "/autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/5.0.7/data/standard/MNI152_T1_2mm_brain"

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Re: [Freesurfer] error in atlas creation
by Anthony Dick 13 Oct '15

13 Oct '15

Hello Bruce, We have tried running the atlas creation on newly freesurfed brains with the latest FS version and keep getting the same error. We have essentially replicated the error we get on our own manually edited volumes by copying the aparc+aseg.mgz and renaming it seg_edited.mgz. Thus, it is unlikely to be a problem with our manually edited brains. This results in the following error at the same place (running the rebuild_gca_atlas.csh script): == Number of threads available to mri_em_register for OpenMP = 16 == reading 23 input volumes... logging results to talairach_one.log reading '<path>/average/RB_one_2015-10-13.gca'... average std = 9.8 using min determinant for regularization = 9.7 0 singular and 426 ill-conditioned covariance matrices regularized reading '<path>/009/mri/nu.mgz'... reading '<path>/average/RB_one_2015-10-13.gca'... reading frame -1 of gca INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() reading '<path>/009/mri/transforms/talairach_one.lta'... mri_read(): couldn't determine type of file <path>/009/mri/transforms/talairach_one.lta mri_em_register: could not open input volume <path>/009/mri/transforms/talairach_one.lta. Perhaps the FS folks could try to replicate this error? You don't need my brains, just a couple of FS'd brains with a file called seg_edited.mgz. If you don't get the error, then maybe it is a problem with our local settings (although we get this error on multiple different computers). Thanks for any help! Anthony On 7/20/15 2:30 PM, Anthony Dick wrote: > Hello, > > I was wondering if these got uploaded correctly. Please let me know if > I made a mistake and thanks, > > Anthony > > On 7/9/15 1:41 PM, Bruce Fischl wrote: >> sure >> On Thu, 9 Jul 2015, Anthony Dick wrote: >> >>> Hello Bruce, >>> >>> I am still getting this error after re-running autorecon1 in the newest >>> version of FS. Can I upload two brains and see what is the issue? I'm a >>> bit stumped on this one. >>> >>> Anthony >>> >>> On 5/26/15 12:21 PM, Bruce Fischl wrote: >>>> Hi Anthony >>>> >>>> sorry, I know you've posted this before. What version are you running? >>>> And what type is your labeled data? That is, are they uchar? int? >>>> At some >>>> point this used to not work with non-uchar data, but I think I >>>> fixed it a >>>> while ago. YOu might try downloading a beta of V6 and see if it >>>> fixes your >>>> problem >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Tue, 26 >>>> May 2015, Anthony Dick wrote: >>>> >>>>> Hello, >>>>> >>>>> I have been stumped by this error I keep getting using the >>>>> rebuild_gca_atlas.csh script. I am trying to build a cerebellar >>>>> atlas, >>>>> so I am wondering if the problem is with the brains we >>>>> parcellated, or >>>>> with my installation etc. The brains consist of manually segmented >>>>> cerebellums from the original T1. The T1 is run through >>>>> Freesurfer, and >>>>> the ROIs are made in Freeview. The edited file is called >>>>> seg_edited.mgz. >>>>> Things run smoothly up until this error: >>>>> >>>>> using MR volume /<path>/subjects/4/mri/brain.mgz to mask input >>>>> volume... >>>>> reading 23 input volumes... >>>>> logging results to talairach_one.log >>>>> reading 'subjects/average/RB_one_2015-05-14.gca'... >>>>> gcaAllocMax: node dims 32 32 32 >>>>> gcaAllocMax: prior dims 128 128 128 >>>>> gcaAllocMax: max_labels 0 >>>>> average std = 8.4 using min determinant for regularization = 7.1 >>>>> 0 singular and 119 ill-conditioned covariance matrices regularized >>>>> reading '/<path>/subjects/4/mri/nu.mgz'... >>>>> reading '/<path>/subjects/average/RB_one_2015-05-14.gca'... >>>>> gcaAllocMax: node dims 32 32 32 >>>>> gcaAllocMax: prior dims 128 128 128 >>>>> gcaAllocMax: max_labels 0 >>>>> reading frame -1 of gca >>>>> MRIcopyFrame: src and dst must be same type >>>>> reading '/<path>/subjects/4/mri/transforms/talairach_one.lta'... >>>>> mri_read(): couldn't determine type of file >>>>> /<path>/subjects/4/mri/transforms/talairach_one.lta >>>>> mri_em_register: could not open input volume >>>>> /<path>/subjects/4/mri/transforms/talairach_one.lta. >>>>> >>>>> >>>> _______________________________________________ >>>> 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. >>>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Anthony Steven Dick, Ph.D. Assistant Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu Webpage: faculty.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu Join the Society for the Study of Human Development: http://www.sshdonline.org

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