Freesurfer

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30098 discussions

Processing of young children using Freesurfer
by Zoellner, Frank 11 Feb '16

11 Feb '16

Hi, I am currently working on a project involving brain morphometry of 2 year old children. We are interested in segmenting the ventricle and I tried to run freesurfer using the standard recon-all -all for a first test. Unfortunately, freesurfer reports an error (see attached log file). I also read about that it is advised to run freesurfer with patient age >5 but maybe someone has an idea how to solve this. As far as I get from the step it crashes at the intensity correction step? Do I need to calculate some sort of template maybe ? Any comments welcome Yours Frank ---------------- PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner(a)MedMa.Uni-Heidelberg.de<mailto:Frank.Zoellner@MedMa.Uni-Heidelberg.de> Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

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Re: [Freesurfer] To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 10 Feb '16

10 Feb '16

If I use: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/subj/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz --fill-ribbon ERROR: Option --fill-ribbon unknown ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 8-feb-2016 20.35 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST Thanks.I have down a right ad left ROI on the surface.Next, I have run: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gzmri_label2vol --label ramgseed_lhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o LEFT_ROI.nii.gz mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgzmri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest -mean -cfg RIGHT_ROI.configfcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest -mean -cfg LEFT_ROI.config fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config fcseed-sess -s subj1_FS -cfg LEFT_ROI.config but during fcseed-sess this error occurs: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $cwd cmdline mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh sysname Darwinhostname iMac-di-Stefano.localmachine x86_64user StefanoUseRobust 0Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gzLoading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gzVoxel Volume is 64.5752 mm^3Generating list of segmentation idsFound 1 segmentationsComputing statistics for each segmentation 0 1 0 0.000MRIalloc(0, 1, 1): bad parmReporting on 0 segmentationsComputing spatial average of each frameWriting to /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mghSegmentation fault ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 8-feb-2016 4.38 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST Use mri_label2vol to convert the label into a volume in the anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make sure to use --fill-ribbon if the label is surface-based. When running fcseed-config, specify the volume with the -seg option and use -segid 1 On 2/7/16 3:16 PM, stdp82(a)virgilio.it wrote: 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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difference in 001.mgz found
by Krieger, Donald N. 10 Feb '16

10 Feb '16

These runs were executed on the Open Science Grid. So the data file, the scan, was uploaded to grid worker machine, placed in a transitory directory, and processed. The full pathname of the file is included in 001.mgz. I got it by: zcat mri/orig/001.mgz | strings Here are the input and output file names for 2 of the runs: /var/lib/condor/execute/dir_31034/MRN_1_defaced.mgz /scratch/tmp.FFTGBhmgp8/MRN_1/mri/orig/001.mgz /var/lib/condor/execute/dir_3734674/glide_HRFaAm/execute/dir_3741395/MRN_1_defaced.mgz /scratch/tmp.ghJfB4leGR/MRN_1/mri/orig/001.mgz Best - Don > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer- > bounces(a)nmr.mgh.harvard.edu] On Behalf Of Krieger, Donald N. > Sent: Wednesday, February 10, 2016 6:38 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] comparing multiple runs on the same scan > > It looks like they do give the same results. > I have to write something to go through everything systematically which I may > not get to till tomorrow. > Also I am checking to see whether there was some difference in how 001.mgz > was created. > The source image file on which we are running freesurfer is a defaced.mgz . > It's possible that it was sitting in a different directory for the different runs > since the runs were executed by a work flow management system (Pegasus) on > the Open Science Grid. > > Don > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer- > bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [greve(a)nmr.mgh.harvard.edu] > Sent: Wednesday, February 10, 2016 6:13 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] comparing multiple runs on the same scan > > That probably means that there is something in the header that is different. It > should print a report to the terminal. Do they not give the same results? > > On 02/10/2016 04:36 PM, Krieger, Donald N. wrote: > > mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are > different. > > In fact, their sizes are slightly different. > > > > > > > >> -----Original Message----- > >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer- > >> bounces(a)nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > >> Sent: Wednesday, February 10, 2016 3:45 PM > >> To: Freesurfer support list > >> Subject: Re: [Freesurfer] comparing multiple runs on the same scan > >> > >> Hi Don > >> > >> are you saying the 001.mgz is different when created from the same > >> dicom data? Can you run mri_diff on it to see what the difference is? > >> > >> cheers > >> Bruce > >> On Wed, 10 > >> Feb 2016, Krieger, Donald N. wrote: > >> > >>> We would like to confirm that we are getting identical results from > >>> multiple freesurfer runs on the same data set. > >>> > >>> To do so we are comparing identically named files using md5sum and > >>> would very much appreciate your thoughts on our results. For > >>> multiple files, we concatenate them and pipe the output into md5sum. > >>> Below is a table showing what we’ve found so far. I take hope from > >>> the positive matches we get from all of the .annot files and from > >>> the fact that 001.mgz does not match. This latter suggests that > >>> there is a date or something embedded in some of the files from > >>> separate runs which > >> defeats the match. > >>> > >>> > >>> Please let us know what you know about this and thanks. > >>> > >>> > >>> > >>> file(s) > >>> > >>> md5sum result > >>> > >>> label/*.annot > >>> > >>> match > >>> > >>> label/*.label > >>> > >>> match > >>> > >>> mri/wmparc.mgz > >>> > >>> mismatch > >>> > >>> surf/qsphere.nofix > >>> > >>> surf/rh.sphere > >>> > >>> mismatch > >>> > >>> mri/orig/001.mgz > >>> > >>> mismatch > >>> > >>> mri/transforms/talairach.m3z > >>> > >>> match > >>> > >>> mri/transforms/talairach.m3z.inv.x.mgz > >>> > >>> mri/transforms/talairach.m3z.inv.y.mgz > >>> > >>> mri/transforms/talairach.m3z.inv.z.mgz > >>> > >>> mismatch > >>> > >>> mismatch > >>> > >>> mismatch > >>> > >>> > >>> > >>> Best - Don > >>> > >>> > >>> > >>> > >>> > >>> Don Krieger, Ph.D. > >>> > >>> Department of Neurological Surgery > >>> > >>> University of Pittsburgh > >>> > >>> > >>> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > 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/ > > _______________________________________________ > 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

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comparing multiple runs on the same scan
by Krieger, Donald N. 10 Feb '16

10 Feb '16

We would like to confirm that we are getting identical results from multiple freesurfer runs on the same data set. To do so we are comparing identically named files using md5sum and would very much appreciate your thoughts on our results. For multiple files, we concatenate them and pipe the output into md5sum. Below is a table showing what we've found so far. I take hope from the positive matches we get from all of the .annot files and from the fact that 001.mgz does not match. This latter suggests that there is a date or something embedded in some of the files from separate runs which defeats the match. Please let us know what you know about this and thanks. file(s) md5sum result label/*.annot match label/*.label match mri/wmparc.mgz mismatch surf/qsphere.nofix surf/rh.sphere mismatch mri/orig/001.mgz mismatch mri/transforms/talairach.m3z match mri/transforms/talairach.m3z.inv.x.mgz mri/transforms/talairach.m3z.inv.y.mgz mri/transforms/talairach.m3z.inv.z.mgz mismatch mismatch mismatch Best - Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh

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error in motion correction
by Ji Won Bang 10 Feb '16

10 Feb '16

Dear. Freesurfer team. Hi. I'm using freesurfer 4.5 version. While doing the motion correction, an error occurred. the command I used: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 the error I have: /home/jbang/Projects/replay/epi/replay01/bold_retino 3dvolreg -verbose -dfile 025/fmc.mcdat -base 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 degrees from plumb. ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees from plumb. ++ centers of base and input datasets are 9.09 mm apart ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't have same dimensions! Input: nx=74 ny=74 nz=32 Base: nx=74 ny=74 nz=33 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. I think it's because the volume size is different. The volume size for bold_retino is: number of slices 32 The volume size for bold_decode: number of slices 33 What should I do to correct this error? Thank you for taking your time. Best, Ji Won

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Middle cerebellar peduncle segmentation
by Henri Pazro 10 Feb '16

10 Feb '16

Dear experts, I'm trying the brainstem segmentation from Juan Eugenio Iglesias and would like to know if the middle cerebellar peduncle will be added in a near future? Thanks! H.

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FS 5.3 and OS X 10.11
by prasser 10 Feb '16

10 Feb '16

Hi, On the download page it mentions that Freesurfer v5.3 is not compatible with OS X 10.11 because of an implementation of SIP. As a test, I have run a few subjects with v5.3 under OS X 10.11.3 with SIP enabled but was unable to see any problems, with all test subjects completing without error. I was wondering what I should be looking for (i.e. in the .log etc?) that would indicate that v5.3 is not compatible with OS X 10.11.3. Thanks.

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Free surfer- correcting for head size
by Christina van den Brink 10 Feb '16

10 Feb '16

Hello, I have a question regarding volume-correction for the morphometry stats obtained via recon-all. I’ve noted that eTIV is derived using the atlas scaling factor in order to account for head size. I’m wondering whether the other volumes given, e.g. TotalGray or lhCorticalWhiteMatter, have also been corrected for head size? If not, is there a recommended method in which to do so so that regional volumes can be compared between participants? Many thanks for your help! Best, Christina

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Re: [Freesurfer] Tracula_weighted dti metrics values
by Anastasia Yendiki 09 Feb '16

09 Feb '16

Hi John - The values are weighted (multiplied) by the probability distribution (path.pd.nii.gz) at the same voxel. So they are the expected values, from a probabilistic standpoint. The distribution is thresholded at 20% of its maximum by default (this is a parameter in dmri_pathstats). Best, a.y On Wed, 16 Sep 2015, John Anderson wrote: > Hi Anastasia, > How the script "dmri_pathstats" compute the weighted FA, MD, AD, and RD > values? > I checked the command "dmri_pathstats" inside the file "trac-all.log" but I > was unable to figure out how this weighting is working. Is it by multiplying > the mean DTI metrics by the number of voxel? > > If my FA maps is "dtifit_FA.nii.gz" and my probabilistic distribution map > for the cortico spinal tract is "path.pd.nii.gz" and I want to compute FA > value using the command "fslstats" like: > > fslstats dtifit_FA.nii.gz -k path.pd.nii.gz -m ==== >This command will > output the mean FA for the probabilistic distribution map. How can I weight > this FA value using the previous command line? > > Bests, > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > >

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Combining lh. and rh. surfaces
by Maheen Siddiqui 09 Feb '16

09 Feb '16

Dear FreeSurfer Users, I have been using the recon-all FreeSurfer command to reconstruct surfaces from T1 weighted MRI scan. I need to import the surfaces I have into Homer2 Atlas Viewer and for this I need whole surface/volume files rather than the individual hemispheres. Does anybody have experience combining the hemispheres? Many thanks, Maheen Maheen Siddiqui BBSRC LIDo PhD Student Centre for Brain and Cognitive Development Birkbeck, University of London London

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