Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

sub field hippo segment fault in kvlSegmentHippocampalSubfields.sh: line 18
by Knut J Bjuland 19 Aug '12

19 Aug '12

When I run recon-all for subfield segmentation I get a segmentation error? I get the error message below. Cheers Knut J Bad trial move (maximal deformation: 278.205, lambda: 12.021) Cost going from 433597 to 1.79769e+308 Transforming mesh Done transforming mesh Increasing lambda from 12.021 to 24.0421 and trying again. Transforming mesh Done transforming mesh Calculating Levenberg-Marquardt step with lambda 24.0421... Time taken to solve the Levenberg-Marquardt system of equations: 0.621659 ...done! maximalDeformation: 348.155 Transforming mesh Done transforming mesh Rasterizing Levenberg-Marquardt... Done transforming mesh Rasterizing Levenberg-Marquardt... /global/apps/freesurfer/5.1.0/bin/kvlSegmentHippocampalSubfields.sh: line 18: 21317 Segmentation fault kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt failed to do kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt Linux c4-1.local 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:50:31 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subject_id exited with ERRORS at Sat Aug 18 19:00:37 CEST 2012 For more details, see the log file /home/kjbjuland/freesurfer/20_ucsd_automatic/023/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

1 1

mris_make_template needing .H file
by Sourena Soheilinezhad 19 Aug '12

19 Aug '12

Hi experts, I have tried this syntax for making a surface template: mris_make template ?h sphere subj1 subj2 subj3 my_template.tiff Output is an error saying "Could not read curvature file: ?h.infalted.H" But searching in the /surf directory for .H file, I have added "-infname white_avg" to the command and it seems to run smoothly. My question is, what is this .H file? Should I safely ignore the default search for inflated.H and keep on using white_avg.H instead? Also, the make_average_surface command gives the same "missing .H file" error but this time there is no -infname parameter to be manipulated. Thanks in advance, Sourena

2 4

How TE, TI and flip angle parameters affect the images and results?
by Daniel Ferreira 18 Aug '12

18 Aug '12

Dear all, We are designing a study based on clinical data. We want to work with a MPRAGE sequence but subjects have been given 4 different sets of parameters: - TR: 1900; TE: 4,38; TI: 1100; flip angle: 15 - TR: 1900; TE: 3,55; TI: 1100; flip angle: 15 - TR: 1900; TE: 3,39; TI: 900; flip angle: 9 - TR: 1900; TE: 3,39; TI: 900; flip angle: 15 I wonder how these differences could affect the images and thus the results. Can I combine all of them or at least some of them? Are they so different that I should just study them by separate? thank you very much on advance Daniel Ferreira

3 2

editing segmentation
by carolina.mr 17 Aug '12

17 Aug '12

1 0

moving volumetric masks to surface labels within subject
by Alex Kell 17 Aug '12

17 Aug '12

hi freesurfers, i'm trying to move a volume from a subject's native anatomical space to that subject's surface space, and i'm running into some difficulty. we have binary masks in each subject's native anatomical space and we'd like to move these to be labels in that subject's surface space. there we'd edit them (either manually or with dilation and erosion) and extract some simple anatomical measures (like thickness) from that region in the surface space. to do this, i am using mri_vol2surf to get the volume in the subject's surface space, and then using mri_cor2label to convert this surface file to a label. the problem is that when i look at the label in the surface space, it is in clearly the wrong position -- even though when i look at the volumetric mask as an overlay in tksurfer it looks like it's in the position that it's supposed to be. for instance, see the attached. magenta is the volumetric mask overlay (in the correct position) and the blue-red circle is the label file (in the wrong position). my calls: mri_vol2surf --mov <volumetric_mask> --reg identity.dat --hemi rh --inflated --o <output_surf_file> mri_cor2label --i <output_surf_file> --id 1 --l ./<surf_label> --surf <subj> rh inflated "identity.dat" is a tkregister-style registration matrix where i just put ones on the diagonal and zeros everywhere else. i also tried mri_vol2surf where i used the --regheader flag. any thoughts? what's going on here? thanks in advance. alex

3 11

Philips dicom - error unpacksdcmdir
by iacono＠nmr.mgh.harvard.edu 17 Aug '12

17 Aug '12

Hi, I've been trying to sort some dicom and to convert them into nifti volumes. I am using the command: unpacksdcmdir -src $source -targ $target -fsfast -scanonly series.txt but the process gives me this error: Log file created by unpacksdcmdir $Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $ /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/unpack.log /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI Thu Aug 16 15:27:30 EDT 2012 -src /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM -targ /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI -fsfast -scanonly series.txt mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/16-19:27:30-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400 FreeSurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux SkipMoCo 0 dicomdir /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM Scanning source directory ... INFO: summary file is /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/dicomdir.sumfile INFO: status file is /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/parse.status mri_parse_sdcmdir --sortbyrun --d /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM --o /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/dicomdir.sumfile --status /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/parse.status INFO: scanning path to Siemens DICOM DIR: /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM INFO: Found 2054 files in /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM INFO: counting Siemens Files $Id: mri_parse_sdcmdir.c,v 1.21 2011/03/02 00:04:23 nicks Exp $ cwd /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI cmdline --sortbyrun --d /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM --o /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/dicomdir.sumfile --status /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/NIFTI/parse.status sysname Linux hostname FreeSurfer machine i686 user virtualuser INFO: found 0 Siemens Files ERROR: scanning directory /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM Done scanning Thu Aug 16 15:35:00 EDT 2012 ------------------------------------------ ERROR: no dicom files found in /home/virtualuser/windows-ubuntu/CP_project/DATA/FDA_20120717_JWzp/FDA_20120717_JW/DICOM Then I decided to use directly MRI_convert with a random first_dicom_file just to understand better what was the problem and the process gives me a new error: mri_convert DICOM/IM_0002.dcm prova.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from DICOM/IM_0002.dcm... Starting DICOMRead2() dcmfile = DICOM/IM_0002.dcm dcmdir = DICOM Ref Series No = 301 Found 2055 files, checking for dicoms WARNING: tag SeriesNumber not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found Found 351 dicom files in series. WARNING: tag SeriesNumber not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found WARNING: tag ImageNumber not found WARNING: tag image orientation not found First Sorting Computing Slice Direction Vs: 89.4924 -139.133 124.026 Vs: 0.432834 -0.672923 0.599858 Second Sorting Counting frames nframes = 1 nslices = 351 ndcmfiles = 351 MRIalloc(0, 0, 351): bad parm No such file or directory ERROR: mri alloc failed I saw that other people had a similar problem in the past: my images come from a Philips Achieva 3T, and this is probably the problem (or I am doing something wrong). However I did not find any solution in the old threads of the mailing list. I can send one dicom file if this can help. Thank you Maria

2 1

Separating Specific Areas from a .nii.gz file
by Sam Carpenter 17 Aug '12

17 Aug '12

Dear life savers, headache relievers and brain science dreamers, PROLOG: I'm trying to separate out some regions from a .nii.gz file. I start with a surface parcellation in .annot (Freesurfer land) that I convert to EXAMPLE.nii.gz using mri_aparc2aseg. THE GOAL: To get a .nii.gz file for each one of these regions. Using fslmaths, I threshold the EXAMPLE.nii.gz file above & below the intensity of that region & save as REGION_name.nii.gz. THE PROBLEM: This method is working for the majority of the regions. But many of the output REGION_name.nii.gz files are completely empty. They are there in the original EXAMPLE.nii.gz but are lost in the thresholding some(how/where). THE SOLUTION: Your kind reply... Thanks very much. -Sam

3 3

Re: [Freesurfer] sulcal depth/cortical folding
by Douglas N Greve 17 Aug '12

17 Aug '12

sorry, it fell through the cracks. Please feel free to resend if I don't get back in a reasonable amount of time... Try this command instead mri_segstats --annot subjectname lh aparc --sum lh.sulc.sum --i surf/lh.sulc the output will be lh.sulc.sum doug On 08/16/2012 07:02 PM, Hugh Pemberton wrote: > Hi Doug, did you get a chance to see my last e mail by the way? The > one below. > Thanks very much indeed, > Hugh > > On 15 August 2012 10:32, Hugh Pemberton <hughpemberton1(a)gmail.com > <mailto:hughpemberton1@gmail.com>> wrote: > > HI Doug, > > I tried the mris_anatomical_stats and may well be doing it wrong > but got this as the result: > > hughp@naoshi-WS:~/freesurfer/subjects$ mris_anatomical_stats -a > ABM/surf/lh.sulc -b ABM lh > computing statistics for each annotation in ABM/surf/lh.sulc. > reading volume /home/hughp/freesurfer/subjects/ABM/mri/wm.mgz... > reading input surface > /home/hughp/freesurfer/subjects/ABM/surf/lh.white... > reading input pial surface > /home/hughp/freesurfer/subjects/ABM/surf/lh.pial... > reading input white surface > /home/hughp/freesurfer/subjects/ABM/surf/lh.white... > CTABfindAnnotation: ct was NULL > No such file or directory > Segmentation fault (core dumped) > > Not sure how to rectify this, any ideas? > > Many thanks again, > Hugh > > > On 15 August 2012 01:42, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Hugh, you can run mris_anatomical_stats passing it the sulc > file as input. This will give you averages within aparc. I'm > not sure what you mean by "measuring cortical folding". What > measure would you accept? There's the sulcal depth and then > there's curvature (?h.curv). There are two types of > "normalization". One is intensity normalization which is a > preprocessing step before the segmentation. "Normalization" is > also refers to intersubject registration. Probably you mean > the latter. > doug > > > > On 08/13/2012 09:56 PM, Hugh Pemberton wrote: > > Hi Doug, > > Thanks so much for getting back to my original question > (have included below) and apologies if my question seems > trivial but I'm a bit of a novice with freesurfer.. I've > found the ?h.sulc file but how do I go about extracting > the sulcal depth measurements? Is there a command like > aparcsstats2table? > > Also, is there a way of measuring cortical folding with > freesurfer? And I've read about the noramlization step but > am still not completely clear on it, is this part of the > segmentation of white/gray surface and pial surface? > > Thanks so much for your help, > Best, > Hugh > > Message: 5 > Date: Sun, 12 Aug 2012 22:25:02 -0400 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > Subject: Re: [Freesurfer] (no subject) > To: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <5028657E.8070908(a)nmr.mgh.harvard.edu > <mailto:5028657E.8070908@nmr.mgh.harvard.edu> > <mailto:5028657E.8070908@nmr.mgh.harvard.edu > <mailto:5028657E.8070908@nmr.mgh.harvard.edu>>> > > Content-Type: text/plain; charset="iso-8859-1" > > The values are in the ?h.sulc file > doug > > On 8/12/12 10:12 PM, Hugh Pemberton wrote: > > Hi, > > > > How can I get sulcal depth measurements from Freesurfer? > > > > Cheers, > > Hugh > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

trac-all -path unable to open merged_ph1samples.nii.gz
by Knut J Bjuland 17 Aug '12

17 Aug '12

The Tracula script has been modifed and adopted to a local cluster. I am now able to run trac-all -prep, but trac-all bails out when I am running trac-all -bedp. Is there any work around since I am using FSL 4.1.9 with Fressurfer 5.1 I am not able to see what went wrong when I am running trac-all -bedp., but when I ran trac-all -path I get this error niiRead(): error opening file merged_ph1samples.nii.gz. Should I adjust the patch I have used to get around this error or should I run bedpostx ro another command before running trac-all -path? Will I be able to use Tracula from Freesurfer 5.2 with recon-all data used with Freesurfer 5.1?

2 2

Error - QDEC
by rajeev krishnadas 17 Aug '12

17 Aug '12

Hi Doug Thanks. Generated a new one.. its ok now.. Cheers Rajeev *Thu Aug 16 11:18:49 EDT 2012* Hi Rajeev, did you look in that file to see if there is anything in it? You can try regenerating the file with recon-all -s subject -segstats doug On 08/16/2012 08:19 AM, rajeev krishnadas wrote: >* Hi*>* Please help..*>* I am getting this error message on QDEC when trying to generate stats *>* table.*>**>* /asegstats2table --common-segs --meas volume --tablefile *>* /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat *>* --statsfile=aseg.stats --subjects a01 a02 a03 a04 a05 a06 a07 a08 a09 *>* a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 p01 p03 p04 p05 p07 p08 *>* p09 p10 p11 p12 p13 p14 p15 p16 p17 p18 p19 p20 p21/*>* /SUBJECTS_DIR : /usr/local/freesurfer/subjects/*>* /Parsing the .stats files/*>* /ERROR: The stats file *>* /usr/local/freesurfer/subjects/a01/stats/aseg.stats is not found or is *>* too small to be a valid statsfile/*>* /Use --skip flag to automatically skip bad stats files/*>* /ERROR: In *>* /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, *>* line 230/*>* /vtkKWQdecApp (0x2852ad20): /*>* / Script: /*>* /vtkTemp2 GenerateStatsDataTables/*>* / Returned Error on line 1: /*>* /Uncaught exception: command failed: asegstats2table --common-segs *>* --meas volume --tablefile *>* /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat *>* --statsfile=aseg.stats --subjects a01 a02 a03 a04 a05 a06 a07 a08 a09 *>* a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 p01 p03 p04 p05 p07 p08 *>* p09 p10 p11 p12 p13 p14 p15 p16 p17 p18 p19 p20 p21/*>* /*>* /*>* /Stack trace: /*>* /Uncaught exception: command failed: asegstats2table --common-segs *>* --meas volume --tablefile *>* /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat *>* --statsfile=aseg.stats --subjects a01 a02 a03 a04 a05 a06 a07 a08 a09 *>* a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 p01 p03 p04 p05 p07 p08 *>* p09 p10 p11 p12 p13 p14 p15 p16 p17 p18 p19 p20 p21/*>* /*>* /*>* / while executing/*>* /"vtkTemp2 GenerateStatsDataTables"/*>**>**>* However, the aseg.stats file is in place for a01.*>**>* I have run these before, but recently i ran a hippo-subfields on a01. *>* I wonder if that has anything to do with this!!*>**>* I wonder if there is a work around.*>**>**>* Cheerio*>**>**>* -- *>* Dr Rajeev Krishnadas MBBS, MD, DipNB, MRCpsych*>* Clinical Lecturer*>* Sackler Institute of Psychobiological Research*>* Southern General Hospital,*>* Glasgow*>* G51 4TF*>**>* *http://tinyurl.com/67ah4vk**>* *http://tinyurl.com/cwec6mf**

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer