Freesurfer March 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
247 discussions

Anonymizing Siemens DICOM files
by Caspar M. Schwiedrzik 21 Mar '14

21 Mar '14

Hi Freesurfer Experts, we are looking for a good way to remove subject names and dates of birth from Siemens DICOM headers. Is there something implemented in Freesurfer? Matlab's Image Processing Toolbox has a function to anonymize DICOM files ( http://www.mathworks.com/help/images/ref/dicomanon.html) but we later run into trouble with unpacksdcmdir when we use that. Thanks, Caspar

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Re: [Freesurfer] Segmentation fault:11 with mris_anatomical_stats
by Rupa Sabbineni 21 Mar '14

21 Mar '14

muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh limiting computations to label /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. computing statistics for each annotation in aparc.a2009s.annot. outputting results to outSUB1_lhVOL2... reading volume /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... reading input surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading input pial surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... reading input white surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Segmentation fault: 11 On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni <asabbineni(a)mrn.org> wrote: > Good morning! > > > I was trying to run the mris_anatomical_stats command and for some > subjects I keep getting Segmentation fault:11 error. > > Some of the posts in the archive suggested that I run the recon-all > command since it usually means that subjects surfaces are out of sync SO I > RERAN RECON_ALL(which created the stats). Then I reran > the mris_anatomical_stats command and got the segmentation fault again. > > > The command im using is > > mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log > outSUB1_lhVOL2 SUB1 lh > > > A little background on the new.label. We got the label by doing a > regression in qdec at FDR 0.05 which created cluster and peak cluster label. > > > Can anyone please provide me some insight on how to trouble shoot this > problem? > > Thank you! > > Rupa > -- Rupa

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Re: [Freesurfer] localgi make_outer_surface
by Douglas N Greve 21 Mar '14

21 Mar '14

Hi Charnjit, that script is Maria's code I think (which is why it is a good idea to post to the list and not to us personally :-) doug On 03/21/2014 07:28 AM, Charnjit Sidhu wrote: > Hi Doug, > > I think the problem is similar to the following post on the mailing lists: > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29476.html > > I think the error "denied: host hostname is no submit host" is being caused when matlab is requested in the make_outer_surface process, if you can tell me where and how matlab is requested in the process I can then add code to run our script that enables matlab to run on our cluster. > > Thanks > > Charnjit > > > > > ________________________________________ > 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: 19 March 2014 15:14 > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] (no subject) > > Hi, I have not idea what is going wrong. I would try goggling that error > msg to see what it means and how it might be fixed > > doug > > > On 03/19/2014 06:32 AM, Charnjit Sidhu wrote: >> Dear freesurfers, >> >> This is the first time I am posting so hope the following makes sense, I don't use freesurfer but manage the installation of freesurfer on our cluster. >> >> We have a user who is trying run a script that submits a recon-all job to our cluster using the -localGI flag: >> >> recon-all -subjid $i -localGI >> >> I know this requires matlab which we have installed on the cluster however we cannot submit matlab within a working node which the submitted node is trying to do, we get the following error: >> >> denied: host "hostname" is no submit host >> >> this message is given when the make_outer_surface script matlab script is submitted within the submitted job. >> >> We have a script that allows matlab to run from within the cluster and have tried to add this as an environment variable to the script: >> >> matlab=matlab_cluster ; export matlab >> source $matlab >> >> But when we add this it still fails with the same error, >> >> Do you know how I can make changed to the script allowing us to run the above script when matlab is called? Or are we missing something from our script? >> >> I have attached the relevant scripts and output sent to me by the user. >> >> Can you help me. >> >> Thanks >> >> Charnjit >> >> >> >> >> _______________________________________________ >> 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. > > > -- 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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tkmedit contrast
by Borzello, Mia 21 Mar '14

21 Mar '14

Hi Freesurfers, I recently coregisered a patient and am trying to visualize the electrodes in tkmedit now, but I'm unable to see them very clearly. The CT has 1mm slices, so I don't think there should be anything wrong with the CT. Is there an option on the gui that deals with the contrast? I attached a picture of the max intensity projection that shows wires but no electrodes. Thanks! Mia B.

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Converting volume from fsaverage to subject space
by Omar Singleton 21 Mar '14

21 Mar '14

Hello Freesurfers, I am interested in taking a volume file that is in fsaverage MNI305 space and converting this volume to each subject's volume. How can this be done? Thanks! Best, Omar

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mris_preproc patch
by N. Medic 21 Mar '14

21 Mar '14

Dear Doug, I would need the mris_preproc patch, however the link provided (ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc) is not working. Is there another way of getting the patch (rather than downloading the new version of FreeSurfer)? Best wishes, Nenad *************** that link should work now doug On 02/07/2013 12:53 PM, Uri Hasson wrote: > Dear Doug, > > We’re still using version 5.1 for a pipeline, and need to send > surface-based measures (volume, area, thickness) to a standard space > for whole-brain analysis. I read you had a patched version of > mris_preproc, but the link saw in an online post (below) doesn’t work. > Is there another link to the utility? > > Thanks, > Uri > > D.G wrote: > --- > Hi Tetiana, thanks for the push. I’ve put a new version of mris_preproc > here: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc > This will implement the fix. > To “install” make a backup of mris_preproc in $FREESURFER_HOME/bin, > then > move the new version. > You should re-run recon-all with -qcache (no need to rerun all of > recon-all). > > doug > ---

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Re: [Freesurfer] Pial surface area
by Anita van Loenhoud 21 Mar '14

21 Mar '14

Hi Bruce, The wm.mgz was created a while ago with an older version, by another student. At the moment I use v5.3.0. Should I recreate wm.mgz with this more recent version, or is there another option? Thank you, Anita

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mri_convert .tar.gz files of dicoms?
by Nate Vack 21 Mar '14

21 Mar '14

Hi, I'm testing mri_convert for our dicom conversion needs; one thing that would be fantastic is to be able to feed it a .tar.gz (or .zip) containing a dicom series we'd like to convert. Is there a way to do that? Alternately, if there were a way to make it use stdin, I could just pipe the output of tar to it. Thanks! -Nate

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Re: [Freesurfer] Pial surface area
by Anita van Loenhoud 21 Mar '14

21 Mar '14

Hi Bruce, See below. Thank you! Anita First I tried: *aloenhoud@somerenserver:/data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050$ *mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial INFO: assuming MGZ format for volumes. computing statistics for each annotation in label/lh.aparc.annot. reading volume /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/mri/wm.mgz... znzTAGskip: tag=1818326118, failed to calloc 541878272 bytes! Cannot allocate memory Then I tried the following: *aloenhoud@somerenserver:/data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050$*recon-all -autorecon3 -subjid 0050 mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial ERROR: Flag mris_anatomical_stats unrecognized. -autorecon3 -subjid 0050 mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial Linux somerenserver.herseninstituut.knaw.nl 2.6.32-431.5.1.el6.x86_64 #1 SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0050 exited with ERRORS at Fri Mar 21 14:49:53 CET 2014

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combine FEAT data with inflated ANATOMY to measure distances
by Milde, Christopher 21 Mar '14

21 Mar '14

Dear Surfers, At moment I'm dealing with a huge dataset, preprocessed (with and without smoothing) and statistically analyzed in FSL FEAT. I used the reg-feat2anat to project functional EPI on inflated MPRAGE (recon-all). Because I'm interested in measuring Euclidian distances between peak voxels, I want to project FEAT EPI-data on cortical flat maps (mris_flatten) or spherical surfaces. è Is it possible to project FEAT-data on flat_maps? è Does mris_pmake* works equally fine on different projections of the EPI to ANATOMY (sphere, flat map) to measure peak/vertex distances? *https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017866.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-April/017866.html> I'm a quite Surfer-newby. So sorry for that maybe stupid question... Thank you in advance, Christopher Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Phone: +49-621-1703-6313 E-mail: christopher.milde(a)zi-mannheim.de Homepage: http://www.zi-mannheim.de/ Office: Forschungs- und Verwaltungsgebäude, Room 230

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Freesurfer March 2014