Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Planum temporale measurement
by Adam David Felton 07 Feb '16

07 Feb '16

Hello, I checked the listserv history, but couldn't find an answer to my question: With the 2009 parcellation scheme, 1) does the planum temporale parcellation include the posterior ascending ramus (which Destrieux et al. 2010 seems to imply) and 2) does the planum temporale include the posterior descending ramus? Thank you! Adam

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Freesurfer v6.0 + edit in v5.3.0 then rerun v6.0
by Tiril Pedersen Gurholt 06 Feb '16

06 Feb '16

Dear Freesurfer Experts, It is my understanding that Freesurfer v6.0 is at the verge of being released. Do you have a tentative v6.0 release data? Also, there is a beta version of Freesurfer v6.0. How stable is it? (Mostly thinking of the recon-all pipeline.) Some of our data has been processed in Freesurfer v5.3.0 (recon-all to structural T1 data) and then manually edited. Is there a downside to rerun this data processed in v5.3.0 (after manual edit) in v6.0? Or is it best (or advisable) to rerun this data from the original T1 data in v6.0 and then do a new round of manual edit? Best regards, Tiril ?? -- Tiril Gurholt Postdoctoral Fellow - Psychosis Research Centre University of Oslo, Norway

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seq.info
by Ji Won Bang 05 Feb '16

05 Feb '16

Dear. Freesurfer team I used dcmunpack to convert DCM to nii. This command didn't generate seq.info (I couldn't find it). I'd like to create one by myself.... Do you know how I can check the scan parameters: sequencename nrows ncols nslcs rowpixelsize colpixelsize slcpixelsize ntrs TR I know that when I use: unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir /scan.info I can get sequencename, nrows, ncols... but then from where can I check the others? Thank you very much. Best, Ji Won

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DTI - Tracula question
by Alan Francis 05 Feb '16

05 Feb '16

Hi Anastasia: I am working on a set of DTI data that were obtained at the Martinos center. The data is in a single nii.gz file. The BVECS and BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file? Should I convert the nii.gz file into Analyze to get at the BVECS/ BVALS? thank you so much, best regards, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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Re: [Freesurfer] TRACULA Longitudinal can't find subject folder
by Deniz Gursel 05 Feb '16

05 Feb '16

Dear Anastasia, Thank you very much for your fast solution. Indeed, I was missing the related folders, I haven’t run the recon-all myself and I copied only the final folder and not the whole as a mistake. Now, I passed that error and got stuck with a new one. In the inter-subject registration step, I get the error: #@# Image corrections Fri Feb 5 14:34:25 CET 2016 mri_convert /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz mri_convert /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii... crypt_gkey = FS1gOHzYgoG2U TR=10443.18, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998789, 0.0474208, 0.0131247) j_ras = (0.0473438, 0.99886, -0.00611764) k_ras = (0.0133998, 0.00548885, 0.999895) writing to /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz... crypt_gkey = FS1gOHzYgoG2U if: Expression Syntax. #------------------------------------- /sw/freesurfer/5.3.0/bin/trac-preproc #------------------------------------- #@# Inter-subject registration (base template) Fri Feb 5 14:34:30 CET 2016 cp /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94/dmri/xfms cp: cannot stat ‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat’: No such file or directory cp: cannot stat ‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat’: No such file or directory Linux slow.mri.tu-muenchen.de 3.7.10-1.40-desktop #1 SMP PREEMPT Thu Jul 10 11:22:12 UTC 2014 (9b06319) x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Feb 5 14:34:30 CET 2016 I am attaching the trac_all.log, trac_all.error and dmrirc for you. Also, before the error, at the image correction step, there is “if: expression syntax” message which I couldn’t figure out why it happens. I looked it up and seems like some Unix error. I encountered it many times, when I was running another cross-sectional study and sometimes it went away magically. Thank you very much for your time and help.

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use as seed a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 05 Feb '16

05 Feb '16

Hi list, I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer.How can I do it?Should I use mri_label2vol? Thanks. Stefano

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tracula preproc complains about missing bvec-file
by Parzer, Peter 05 Feb '16

05 Feb '16

Hi, trying to do my first steps with tracula I got stuck early in the preprocessing step. The DICOM import and preparation for FSL seem to work (mri_convert, mri_probedicom, flip4fsl, fslswapdim, fslorient). But then trac-preproc wants to move a file named dwi_orig_flip.mghdti.bvecs that does not exist. What did I wrong? The command I used was trac-all -prep -c dmrirc The content of the configuration file "dmrirc" was the minimum as described in the tutorial: setenv SUBJECTS_DIR /dat/Hirnreifung/Auswertung/freesurfer set dtroot = /dat/Hirnreifung/Auswertung/freesurfer set subjlist = (3001LT) set dcmroot = /dat/Hirnreifung/Daten/DICOM set dcmlist = (3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm) dcminfo.dat and trac-all.log are in the attachments. Peter

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Re: [Freesurfer] freeview command line generic overlay colormap question
by Gardumi Anna (PSYCHOLOGY) 05 Feb '16

05 Feb '16

Dear all, I am currently trying to automatically generate Freesurfer screenshots and, to this purpose, I need to change the color scale of the surface overlay to "Color Wheel - Inverse" and with specific min and max threshold. Looking for a way to achieve this, I found this thread with similar request, but unfortunately no solution was posted. Thus Heath (who kindly replied to my email) suggested to re-post the question to the entire FreeSurfer community. So far I am able only to set the min max threshold with the following command: freeview -f $SUBJECTS_DIR/subj01/surf/lh.inflated:overlay=/pathToOverlay/MyOverlay.mgh:overlay_threshold=-10,10 Does anybody know the command line to set the overlay color scale to "Color Wheel (Inverse)"? Thank you! Any help is very much appreciated! Best regards, Anna ------------------------- Anna Gardumi Department of Cognitive Neuroscience | Faculty of Psychology & Neuroscience | Maastricht University Postal address: PO Box 616, 6200MD, Maastricht, The Nederlands Visiting address: Oxfordlaan 55, room 2.012, 6229EV anna.gardumi(a)maastrichtuniversity.nl

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(no subject)
by Ачча Чимагомедова 05 Feb '16

05 Feb '16

Hello! My name is Achcha. I am a PhD student of Russian Medical Academy for Postgraduate Education. In my research "Dementia with Lewy bodies" (DLB) I am going to determine the association between the focal atrophy measures on MRI and to compare it with clinical features of DLB. I try to install FreeSurfer on my computer. But I have only Windows Operating System, that's why I have got and installed VirtualBox. Could you please send me detailed instructions and help to install FreeSurfer. Thank you, Kindest regards Achcha Chimagomedova

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Brain stem segmentation-- FS6
by Alshikho, Mohamad J. 05 Feb '16

05 Feb '16

Dear Freesurfer experts, I am working on brain stem segmentation analysis using the new module included in FS6. The analysis ran properly for 38/40 subjects. I have an issue with two subjects. I sent my jobs to the cluster as always using the following command line: pbsubmit -c " recon-all -subjid <SUBJECT ID> -brainstem-structures " -f <email address> & After a while I received an email that the job is done: PBS Job Id: 11020983.launchpad.nmr.mgh.harvard.edu Job Name: pbsjob_2045 Exec host: compute-0-111/3 Execution terminated Exit_status=0 resources_used.cput=00:42:33 resources_used.mem=3220236kb resources_used.vmem=7319444kb resources_used.walltime=00:44:45 I checked the subject's folder /mri/ looking for the files : "brainstemSsLabels.v10.1mm.mgz" , "brainstemSsLabels.v10.mgz" but I was unable to find them. I checked the job history in the cluster and it returns as ( quotation -- the last lines): Resolution level 3 iteration 3 deformation iterations 19 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 0.0097272 voxels in 4.1676 seconds minLogLikelihoodTimesPrior = 1.0786e+07 Resolution level 3 iteration 3 deformation iterations 20 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 0.016365 voxels in 4.1717 seconds minLogLikelihoodTimesPrior = 1.0786e+07 Fitting mesh to image data mask took 2144.0218 seconds Error using kvlAtlas3D_Matlab std::bad_alloc Error in kvlRasterizeAtlasMesh (line 11) Error in segmentSubject (line 1078) Started at Thu Feb 4 15:57:18 EST 2016 Ended at Thu Feb 4 16:41:59 EST 2016 #@#%# recon-all-run-time-hours 0.745 recon-all -s CTRL039 finished without error at Thu Feb 4 16:42:00 EST 2016 It stated that the job was ended properly without errors but the previous lines ( before the final stamp) showed errors and the files "brainstemSsLabels.v10.1mm.mgz" , "brainstemSsLabels.v10.mgz" are missing ... Kindly what I am doing wrong? Any suggestions are highly appreciated !! Mohamad

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