Freesurfer

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30132 discussions

Cannot save edited label
by Jürgen Hänggi 26 Oct '12

26 Oct '12

Dear FS experts I used mri_annotation2label to extract the superior frontal gyrus label from the aparc annotation. I edited (cut plane) this label in tksurfer and then tried to save it using Save Selected Label. However, the whole label is saved including also the part that I have cut away. Any idea what is going wrong here? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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recon-all crash
by Jesse Bledsoe 25 Oct '12

25 Oct '12

Hello experts, Wonder if you could help me with the following error after running "recon-all -all -subjid BT6403 -qcache": ---------- unfolding failed - restoring original position -------------------- 0581: dt=0.112000, rms=0.602 (0.000%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 2 hours, 50 minutes and 30 seconds. /var/local/scratch/bledsoe1/ Desktop/Braintumor/BT_6403/touch/ca_register.touch: No such file or directory. bledsoe1 @ivan:~/Desktop/Braintumor/BT_6403$ Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Any suggestions are much appreciated, Jesse

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znzTAGskip error using mri_em_register
by Kim, Daniel 25 Oct '12

25 Oct '12

Hello FreeSurfer users, I was finally able to compile mri_em_register successfully from source and trying to test the build with subject 'bert', I ran into this error ~/freesurfer/bin# ./mri_em_register -uns 3 -mask $SUBJECTS_DIR/bert/mri/brainmask.mgz $SUBJECTS_DIR/bert/mri/nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca $SUBJECTS_DIR/bert/mri/transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer_4_5_0/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading '/usr/local/freesurfer/subjects/bert/mri/nu.mgz'... znzTAGskip: tag=-8454144, failed to calloc 4286513152 bytes! Cannot allocate memory Has anyone had similar error before? I'm using Ubuntu 10.04 LTS- 64 bit and I've built mri_em_register from scratch using CVS public checkout "-P dev" The test subject was through installing freesurfer 5.1.0 and also same has happened with freesurfer 4.5.0 Any help with this would be again greatly appreciated! Cheers! Danny Kim

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residual after mri_glmfit
by Minjie Wu 25 Oct '12

25 Oct '12

Dear FreeSurfers, I have a question regarding mri_glmfit: Is it possible to get the residual data after mri_glmfit? Thank you very much. Minjie

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mri_ca_register error
by Matt Leonard 24 Oct '12

24 Oct '12

Hello, I'm trying to run a simple recon on a single T1 dataset, and am not interested in any quantitative measures (this is just for data presentation and eventual MRI/CT co-registration). To save time, I tried to skip the CA registration step, but got the following error: #-------------------------------------- #@# CA Reg Inv Wed Oct 24 14:49:20 PDT 2012 /Applications/freesurfer/subjects/CH/mri \n mri_ca_register -invert-and-save transforms/talairach.m3z \n Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 So then I tried skipping all the steps that appear to need the talairach.m3z file, and used this command: recon-all -s CH -autorecon2 -nocanorm -nocareg -normneck -noskull-lta -nocalabel -nosegstats That gave the same error. What am I doing wrong as far as skipping the careg step? Thanks, Matt

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Trac-all Error
by Franklin, Crystal G 24 Oct '12

24 Oct '12

Freesurfer, I am trying to run trac-all –prep and trac-preproc keeps exiting with errors. It keeps saying the unwrappedphasemaps must contain at least two volumes. My data only contains one phase image and 2 magnitude images. Do you know what could be causing this error or how to get around it? Thanks in advance, Crystal

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Re: [Freesurfer] Comparing thickness at vertex level
by Douglas N Greve 24 Oct '12

24 Oct '12

they will have the same number of vertices. They will all be in one file, and each vertex is a vertex in fsaverage space, which each subject vertex being mapped to the closest vertex in surface-based atlas. doug On 10/24/2012 04:34 PM, Gabriel Gonzalez Escamilla wrote: > Thanks Doug, > > Does the surface-based thickness approach make possible to compare > exactly the same vertex across all my subjects? or they will be still > have some differences in the number of vertices among them? > > Gabriel > > > El 24/10/12, *Douglas N Greve * <greve(a)nmr.mgh.harvard.edu> escribió: >> Hi Gabriel, this sounds like a standard surface-based thickness study. >> Or am I missing something? In case it is, you can look at the group >> analysis tutorial. Basically, you run mris_preproc (which puts all of >> your subjects into the fsaverage space and saves a stack of thickness >> maps in a single file), then you smooth it, then you run mri_glmfit. >> >> doug >> >> On 10/24/2012 11:47 AM, Gabriel Gonzalez Escamilla wrote: >> > >> > Dear FreeSurfer experts, >> > >> > I'm wondering if is it possible to make vertex to vertex comparisons >> > for thickness on a group of subjects. In other words, I have a bunch >> > of subjects pre-processed with FS but I would like to make comparisons >> > finding the thickness values at same vertex in all of them. Is this >> > possible with Freesurfer? >> > >> > Given that at the beggining all they have different head/brain sizes, >> > I was thinking that a regristration of the surfaces to the same space >> > (FSaverage) would re-sample my data to match in number of vertex. for >> > this, I think that maybe "mri_surf2surf" is capable of such a thing, >> > and then I would have to search for each vertex, or optionally >> > "mris_preproc" using the "-target FSaverage" flag ||*||*would perform >> > something similar. >> > >> > Please tell me what you think about this? >> > >> > >> > Many thanks in advanced, >> > Gabriel. >> > >> > >> > _______________________________________________ >> > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> _______________________________________________ >> 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. >> > > -- > -------------------------- > PhD. student Gabriel González-Escamilla > Laboratory of Functional Neuroscience > Department of Physiology, Anatomy, and Cell Biology > University Pablo de Olavide > Ctra. de Utrera, Km.1 > 41013 - Seville > - Spain - > > Email: ggonesc(a)upo.es > http://www.upo.es/neuroaging/es/ -- 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

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Re: [Freesurfer] mris_topo_fixer -mgz -warnings -seed 1234
by Anne Uhlmann 24 Oct '12

24 Oct '12

Hi Bruce, I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 on a cluster (which I access via putty). It's the only scan that has some kind of a scanner artifact and that shows this particular problem, therefore I thought there might be a link. Thanks, Anne >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 24/10/2012 13:42 >>> Hi Anne can you cc the list so others can answer? What version are you running? This is something we fixed a while ago cheers Bruce On Wed, 24 Oct 2012, Anne Uhlmann wrote: > Hi Bruce, > > Sorry about that. Please find the recon-all.log file attached. The error > message given there is: ERROR: _FindFacePath: could not find path! > > No rh output is getting produced. > When viewing the brainmask.mgz -surfs, an error message says: rh.white: > could not open file. > > When trying to view rh.orig.nofix, the error message says: rh.pial: no such > file or directory. But the wm outline looks just like the lh one, very > angular but otherwise no defects. Sometimes voxels are included that should > not be white matter and in the occipital area some of the white matter is > excluded. > > I can't say much about the rh.inflated.nofix. I can only view it in tkmedit > and it seems to have some fine disruptions in the occipital area. > > Thanks for your help. > Regards, Anne > > > > > >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 22/10/2012 15:50 >>> > Hi Anne > > can you post the whole recon-all.log file? I don't think you included the > actual error message. Also, you can look at the rh.inflated.nofix and > rh.orig.nofix to see if there are any really big defects in the rh before > fixing. Is no rh output produced? > > Bruce > > On Mon, 22 Oct 2012, Anne Uhlmann wrote: > > > Hi there, > > > > I am having trouble with one of my scans where the right hemisphere is not > > getting included in the analysis from the "Fix Topology rh" point on. This > > is the error message I get: > > > > Linux cnode-2-52 2.6.18-308.el5 #1 SMP Tue Feb 21 20:06:06 EST 2012 x86_64 > > x86_64 x86_64 GNU/Linux > > $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ > > /SCRATCH4/cubic/auhlmann/freesurfer/bin/recon-all > >PWD/lustre/SCRATCH4/cubic/auhlmann/freesurfer/subjects/meth_output_test3/MA > S11 > > 2.12.1107.5.2/scripts > > CMD mris_topo_fixer -mgz -warnings -seed 1234 MAS112.12.1107.5.2 rh > > > > The orig.mgz looks OKish (it's not great) except for some kind of a > scanner > > artifact in 2 slices of the scan. I tried to fix it with control points > and > > making edits to the white matter, but unfortunately it didn't solve the > > problem. I am grateful for any suggestions. > > > > Thank you and best regards, > > Anne > > > > ### > > > > UNIVERSITY OF CAPE TOWN > > > > This e-mail is subject to the UCT ICT policies and e-mail disclaimer > > published on our website at > > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from > +27 > > 21 650 9111. This e-mail is intended only for the person(s) to whom it is > > addressed. If the e-mail has reached you in error, please notify the > author. > > If you are not the intended recipient of the e-mail you may not use, > > disclose, copy, redirect or print the content. If this e-mail is not > related > > to the business of UCT it is sent by the sender in the sender's individual > > capacity. > > > > ### > > > > > > > > > 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. > > ### > > UNIVERSITY OF CAPE TOWN > > This e-mail is subject to the UCT ICT policies and e-mail disclaimer > published on our website at > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 > 21 650 9111. This e-mail is intended only for the person(s) to whom it is > addressed. If the e-mail has reached you in error, please notify the author. > If you are not the intended recipient of the e-mail you may not use, > disclose, copy, redirect or print the content. If this e-mail is not related > to the business of UCT it is sent by the sender in the sender's individual > capacity. > > ### > > > ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ###

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task-related functional connectivity analyses freesurfer 5.1.0
by SHAHIN NASR 24 Oct '12

24 Oct '12

Hi, I was wondering if we can compare "functional connectivity" between blocks within a run as we do for BOLD signal using freesurfer. Current documentation of freesurfer is for resting state and does not consider conditions that experiment is Blocked Design. Similar question has been asked previous but nobody answered (see the link below) https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024394.html Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] recon-all \'expression syntax\' error
by Skyler Gabriel Shollenbarger 24 Oct '12

24 Oct '12

Hi Bruce, I'm having the same error: export SUBJECTS_DIR=$PWD recon-all -subjid freesurfer -autorecon1 if: Expression Syntax. Running on: OS X 10.6.8 using both terminal and X11 (freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0) Thanks in advance, Skyler -- Skyler G. Shollenbarger Graduate Student - UWM Brain Lab Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee

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