Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Longitudinal stream : LME and limits of model
by Matthieu Vanhoutte 14 Dec '18

14 Dec '18

Dear Freesurfer’s experts, I would have some questions regarding the LME model to be used in longitudinal stream: 1) Which are the ratio limits or % of missing timepoints accepted ? (according time, I have less and less subjects time points) 2) Is it possible to include patients that would miss the first timepoint but got the others ? 3) Considering a group in longitudinal study, which is the number of subjects minimal of this group accepted for LME modeling ? 4) Finally, concerning quality control and among a big number of total time points, which essential controls are necessary ? (Control of norm.mgz of the base, alignment of longitudinal timepoints on base,… ?) Best regards, Matthieu

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Yeo 2011 Functional Cortical Parcellations
by Bronwyn Overs 24 Oct '18

24 Oct '18

Hi Mailing List, I am attempting to apply the Yeo 2011 7-network fucntional parcellations to a set of fs MRIs processed with v5.1.0. Below are listed the first three steps I plan to take and I am seeking advice as to: A) Whether this approach is valid. B) Steps to take next. * Steps 1-3: * *1. Run MNI152 1mm template through recon-all* recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS recon-all -all -subjid Yeo2011_MNI152_FS *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space* mri_vol2vol --mov Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:* mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz --nearest --inv-morph When previously mapping the Choi 2012 straital parcellations, steps 4 and 5 were: 4. *Creating a striatal mask in the native subject's space from freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens (26 & 58)*: mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz *5. **Using this mask to mask the choi striatal parcellations* fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz Yeo_atlas_subjID_mask.nii.gz Do I need to do a similar thing for the Yeo cortical parcellations and if so what regions should I include in the cortical mask? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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Morphing Buckner2011 MNI152 to subject's space {Disarmed}
by Peled, Noam 05 Oct '18

05 Oct '18

Dear group, I'm trying to morph the Buckner2011<http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011> cerebellum segmentation map from MNI152 to subject's space: mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --m3z talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest --inv-morph It worked with the 17 networks, but didn't work with the 7 networks version. Any ideas? This is really strange. Thanks, Noam

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Building from source -- autoconf error
by Alle Meije Wink 29 Mar '18

29 Mar '18

I'm trying to build FreeSurfer from source on my Debian 8 (jessie) system. (64 bit, using g++ 4.9 for compilation) After $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev $ cd dev $ cvs update -d # just to make sure $ ./setup_configure I get these messages: rm -rf autom4te.cache libtoolize --force libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `config'. libtoolize: linking file `config/ltmain.sh' libtoolize: putting macros in `m4'. libtoolize: linking file `m4/libtool.m4' libtoolize: linking file `m4/ltoptions.m4' libtoolize: linking file `m4/ltsugar.m4' libtoolize: linking file `m4/ltversion.m4' libtoolize: linking file `m4/lt~obsolete.m4' libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree. aclocal aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: error: configure.in:2045: file 'm4/autotroll.m4' does not exist Which looks like a not-(anymore)supported use of autoconf? I found one previous message on the list about autotroll https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021854.… that provided another version of configure.in which might solve the issue. And it did in the original case but sadly not for me. I get the same error message also with the new configure.in -- there should probably be a configure.ac? If anyone knows how to make this work (e.g. by modifying the configure script) that would be fantastic.

8 17

mris_flatten error: bad vertex
by Ji Won Bang 20 Feb '18

20 Feb '18

Dear. Freesurfer experts. Hi. I'm having a problem with mris_flatten (version 5.3.0) Could you please help me fix this problem? My command line is: mris_flatten -w 0 -distances 12 7 $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat It returns the error: using write iterations = 0 sampling 7 neighbors out to a distance of 12 mm reading patch /home/jbang/Projects/replay/mri//replay06/surf/lh.oc.patch.3d with 30434 vertices (20.5% of total) MRISreadPatch: bad vertex # (148517) found in patch file No such file or directory When making the patch lh.oc.patch.3d, I followed the processes below: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower select 3 points along a boundary between upper and lower visual fields (near calcarine sulcus) and press "Cut line". Then, select 4 points to define the cutting plane: 1 on lower side of the line, 2 on upper side of the line, 3 on the opposite surface (use rotation tool), and 4 to specify which portion of surface is kept, and press "Cur plane". File->Patch->Save Patch As lh.oc.patch.3d So I think I made the patch correctly. ! weird thing that I suspect is that when I click save patch as, the default location is $SUBJECTS_DIR/fsaverage/surf/ , so I had to change it to $SUBJECTS_DIR/$SUBJECT/surf Could you please help me? Thanks a lot! Best, Ji Won

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Nonlinear CVS registration into average brain for coordinates
by Zhou, David Wei 10 Jan '18

10 Jan '18

Hi all, I have a data set of 14 subjects with intracranial (both cortical and subcortical) electrode implants, already recon'ed in Freesurfer, with an average brain + surface computed of these subjects. I would like to map each subject's electrode coordinates (a set of RAS points) into the average brain using a nonlinear transformation to account for individual deviations in surface topology. I'm trying to figure out the steps that must be taken to achieve this. With my average brain as a template, it seems like I would use mri_cvs_register to produce each subject warped onto the template. After generating those warps, how does one apply the same warp to a set of coordinates, for example to find out where my electrodes end up in the template brain? Which output file in .../cvs contains the data necessary to compute the coordinates in the template? I'd appreciate any instruction, thanks! David

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Re: [Freesurfer] [tracula] error running trac-all -prep
by Borsodi Florian 20 Dec '17

20 Dec '17

Hi Anastasia, Yes, i am running this on ubuntu 12.04. Sincerely, Florian >>> Anastasia Yendiki 20.08.13 17.38 Uhr >>> Hi Florian - Are you running this on an ubuntu system by any chance? a.y On Tue, 20 Aug 2013, Borsodi Florian wrote: > Hi Anastasia, > > Thank you for your help. > I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the command "xfmrot" changed the dots back to > commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing the > system language everything was genereted correctly and trac-all -prep ran without any errors. > I'm so glad. > > Then, I started the next step "trac-all -bedp" and got a syntax error "/usr/local/freesurfer/bin/bedpostx_mgh: 131: > /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. " I also attached the the logfile. I was reading > about this error in the mail archive. Would I have to run "bedpostx" outside of tracula ? > > Sincerely, > Florian > > >>> Anastasia Yendiki 19.08.13 17.54 Uhr >>> > > Hi Florian - Can you please change the decimal commas to points and try > again? > > a.y > > On Mon, 19 Aug 2013, Borsodi Florian wrote: > > > Hi Anastasia, > > > > Here are the bvec and bval files you asked me about. > > > > Sincerely, > > Florian > > > > >>> Anastasia Yendiki 18.08.13 22.52 Uhr >>> > > > > Hi Florian - Can you please also attach the bvecs/bvals files from the > > dmri directory? > > > > Thanks, > > a.y > > > > On Sun, 18 Aug 2013, Borsodi Florian wrote: > > > > > Hi Anastasia, > > > > > > Thanks for your help. I renamed the directories and reran trac-all. It > > > worked for the moment. > > > However, then I got another error: "bvecs and bvals don't have the same > > > number of entries." > > > I don't know why, because they actually have the same number of entries. > > > > > > I attached the logfile so that you may see what is going on. The error > > > occours at line 1463. > > > > > > Thank you in advance for your help. > > > > > > Sincerely, > > > Florian > > > > > > > > > >>> Anastasia Yendiki 15.08.13 18.01 Uhr >>> > > > > > > Hi Florian - I see what's going on. Can you please rename the directory > > > /data/physics/florian/nii into something that doesn't include "nii", and > > > rerun? Because "nii" is a file extension, this confuses some of the > > > scripts. > > > > > > Thanks, > > > a.y > > > > > > On Thu, 15 Aug 2013, Borsodi Florian wrote: > > > > > > > Hi Anastasia > > > > > > > > I ran the command you sent me and it runs without any errors. > > > > I also attached the command line for you. > > > > > > > > Furthermore i ran data with 12 diffusion directions and i keep getting the > > > > same kind of problems. > > > > > > > > sincerely > > > > Florian > > > > > > > > >>> Anastasia Yendiki 02.08.13 19.59 Uhr > > > >>> > > > > > > > > Hi Florian - Can you please run this command directly on the command line > > > > and see if there are any errors? > > > > > > > > flip4fsl > > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz > > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz > > > > > > > > Thanks, > > > > a.y > > > > > > > > On Fri, 2 Aug 2013, Borsodi Florian wrote: > > > > > > > > > Hi Anastasia > > > > > > > > > > Thank you for your answer. > > > > > > > > > > Yes, those files exist. > > > > > I also extracted the bvec an bval files with anotther software then > > > > dcm2nii > > > > > and i keep getting the same kind of error. > > > > > Also, about the 6 diffusion direction, those data i sent you, are just > > > > > testdata for running tracula. > > > > > > > > > > sincerely > > > > > Florian > > > > > > > > > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr > > > >>> > > > > > > > > > > Hi Florian - Do these files exist? > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvec > > > s > > > > > > > > > > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bval > > > s > > > > > > > > > > > > > > > > > > > The format of the bvecs and bvals that you sent seems fine, but (and > > > this > > > > > has nothing to do with the error you're getting) I have to warn you that > > > > > you may not be able to get good results running probabilistic > > > tractography > > > > > on this data. It looks like you're acquiring the same 6 diffusion > > > > > directions, repeated 8 times. Six directions is the absolute minimum for > > > > > reconstructing the tensor model, but will probably not be sufficient for > > > > > the crossing fiber model that bedpostx reconstructs (and is used by > > > > > tracula). Your scan time is better spent acquiring 48 different > > > > > directions, rather than the same 6 directions 8 times. > > > > > > > > > > a.y > > > > > > > > > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > > > > > > > > > Hello, > > > > > > > > > > > > I have been trying to run tracula on my data and i keep getting the > > > same > > > > > > kind of error repeatedly. > > > > > > For my imput I am using dicoms from a Siemens scanner with a stadard > > > > > > diffusion protocol. However, tracula cannot read the bvec and bval > > > data > > > > > out > > > > > > of the dicom header. Therefore, I implemented bvec and bval files into > > > > the > > > > > > config file. > > > > > > After doing so, I got the error which says that tracula cannot find > > > the > > > > > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > > > > > I have tried many options, but still cannot find a solution. > > > > > > I am hoping to get some troubleshooting help. > > > > > > > > > > > > I have atteched my log- and config- files, as well as my bvec and bval > > > > > > files. > > > > > > To uphold patient confidentiality, I have encode the name patient's > > > data > > > > > as > > > > > > "AAAAAA". > > > > > > > > > > > > I believe the problems are the bvec and bval files or their > > > structures. > > > > > The > > > > > > log-file lete me assume this, especially the lines 202 - 205, 264 - > > > 268 > > > > > and > > > > > > 1480 - 1484. > > > > > > > > > > > > Thank you in advance for your help, and your speedy response. > > > > > > > > > > > > With kind regards, > > > > > > > > > > > > Florian Borsodi > > > > > > Department of Neurology > > > > > > Medical University of Graz > > > > > > > > > > > > > > > > > > > > > > > > > > > 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 > > > > > > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing
by Elijah Mak 03 Aug '17

03 Aug '17

Hi ZK, Thanks. It is great news! I would like to report the following. asegstats2table seems to be acting strangely. File "/Applications/freesurfer_b6/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' Even typing asegstats2table --help leads to the same error message. It was not found in a prev dev built or in 5.3. Thanks. Also, not sure if it's placebo, but freeview seems to be running quicker now. Best Wishes, Elijah

4 3

output with input matrix size and referential
by pierre deman 02 Aug '17

02 Aug '17

Hello, I am trying to have the atlases aparc.a2009+aseg.mgz, hippocampal subfield etc ... in a matrix with the same size as the input of recon-all (and not the cubic matrix 256x256x256) and with the same orientation. what is the best way to do it ? Cheers, Pierre -- DEMAN Pierre Mobile : +33 7 82 57 80 94

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Freesurfer December 2016