Freesurfer September 2012

freesurfer@nmr.mgh.harvard.edu

89 participants
154 discussions

Anatomical variation between individual surface and average template
by liang wang 14 Sep '12

14 Sep '12

Dear FS folkers, I am working on a functional probabilistic atlas. I find that some functional regions (particular along a big sulcus) show quite high probability value over a large sample, whereas the probability for some regions are quite lower. I think this disparity could be accounted for by the anatomical variation on each surface node that appears while surface-based registering individual surface to the average template that was provided by Freesurfer. For instance, the anatomical variation could be pretty small within a big sulcus (like central sulcus). I assume that Freesurfer output a file which characterizes this type of anatomical variation. Could someone point me which file it is and how to use it to create a group-level measure in order to clear display somewhere has large variation. Thanks. Best, Liang -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540

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Re: [Freesurfer] ERROR: You are trying to re-run an existing subject
by Douglas N Greve 14 Sep '12

14 Sep '12

what did you rename it to and what is your command line after you rename it? On 09/14/2012 04:48 PM, Carolina Valencia wrote: > As I said in the first email I tried the suggestions in the message, > rename the files, folders, eliminate the folders, starts from scratch > etc and again with your answer, I rename the folder of dicom, and > rename the MPRAGE files and anything works, still the same message. > Thank you, > > > 2012/9/14 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > The error output below tells you what to do. If the subject folder > (HPTU_vol11_2012) already exists. Since it has your dicom data in > it, you should not delete it. Instead, rename that directory and > keep your command-line (changing the -i path to point to the new > dicom file but keeping the same subject name), or change the name > of the subject. > doug > > > > > On 09/14/2012 03:44 PM, Carolina Valencia wrote: > > the directory exists and trying without / doesn't change anything, > any advice? > One week ago, I was processing with the same command line with > other subjects without problems, > > 2012/9/14 Douglas N 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>>> > > > And before you run this, does > $SUBJECTS_DIR/HPTU_vol11_2012 exist? > BTW, try it without a slash at the end of the name. > doug > > > On 09/14/2012 02:09 PM, Carolina Valencia wrote: > > > Sure! > > cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria$ > recon-all -s HPTU_vol11_2012/ -i > HPTU_vol11_2012/dicom/MPRAGE.Ser1.Img0.dcm > > 2012/9/14 Douglas N 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>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > What is your command line? > doug > > > > On 09/14/2012 12:23 PM, Carolina Valencia wrote: > > Hi Freesurfer users: > > > > I'm trying to run recon-all command in a single subject and > > I don't know why always there is an error message about the > names, I > > tried the suggestionsin the message, rename the files, folders, > > eliminate the folders etc > > But I don't succeed to star to running my data. > > Many thanks, > > > > > > ERROR: You are trying to re-run an existing subject with > (possibly) > > new input data (-i). If this is truly new input data, you > should delete > > the subject folder and re-run, or specify a different > subject name. > > If you are just continuing an analysis of an existing > subject, then > > omit all -i flags. > > > > -- > > -- > > *Carolina Valencia Muñoz* > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > -- > > > -- > 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> > > > -- 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] ERROR: You are trying to re-run an existing subject
by Douglas N Greve 14 Sep '12

14 Sep '12

The error output below tells you what to do. If the subject folder (HPTU_vol11_2012) already exists. Since it has your dicom data in it, you should not delete it. Instead, rename that directory and keep your command-line (changing the -i path to point to the new dicom file but keeping the same subject name), or change the name of the subject. doug On 09/14/2012 03:44 PM, Carolina Valencia wrote: > the directory exists and trying without / doesn't change anything, > any advice? > One week ago, I was processing with the same command line with other > subjects without problems, > > 2012/9/14 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > And before you run this, does $SUBJECTS_DIR/HPTU_vol11_2012 exist? > BTW, try it without a slash at the end of the name. > doug > > > On 09/14/2012 02:09 PM, Carolina Valencia wrote: > > > Sure! > cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria$ > recon-all -s HPTU_vol11_2012/ -i > HPTU_vol11_2012/dicom/MPRAGE.Ser1.Img0.dcm > > 2012/9/14 Douglas N 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>>> > > > What is your command line? > doug > > > > On 09/14/2012 12:23 PM, Carolina Valencia wrote: > > Hi Freesurfer users: > > > > I'm trying to run recon-all command in a single subject and > > I don't know why always there is an error message about the > names, I > > tried the suggestionsin the message, rename the files, folders, > > eliminate the folders etc > > But I don't succeed to star to running my data. > > Many thanks, > > > > > > ERROR: You are trying to re-run an existing subject with > (possibly) > > new input data (-i). If this is truly new input data, you > should delete > > the subject folder and re-run, or specify a different > subject name. > > If you are just continuing an analysis of an existing > subject, then > > omit all -i flags. > > > > -- > > -- > > *Carolina Valencia Muñoz* > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <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> > > > > > -- > -- -- 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] ico4 parcellation and mri_segstats
by Douglas N Greve 14 Sep '12

14 Sep '12

It looks like there are several (102 to be exact) that do not have any voxels in your parcellation. Eg, #82: 82 82 ic4.tri_vertex_82 0 So the problem appears to be with mris_make_face_parcellation, not with mri_segstats. doug On 09/10/2012 10:56 AM, Linda Douw wrote: > Hi Doug, > Output and sumfile are attached. Any ideas? > Linda > >> Message: 10 >> Date: Mon, 13 Aug 2012 15:55:13 -0400 >> From: Douglas N Greve<greve(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10 >> To: freesurfer(a)nmr.mgh.harvard.edu >> Message-ID:<50295BA1.8090307(a)nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi Linda, can you send the terminal output for mri_segstats? Can you >> also send the summary file? >> doug >> >> On 08/13/2012 10:59 AM, Linda Douw wrote: >>> Hi Doug, >>> >>> I first parcellate fsaverage5 using ico4 (all my functional data are >>> morphed to fsaverage5 surface): >>> >>> mris_make_face_parcellation /fsaverage5/rh.inflated >>> $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot >>> >>> Then I extract the waveforms using mri_segstats >>> >>> mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot >>> fsaverage5c rh ico4 --sum ico4_rh.sum >>> >>> Hope this clarifies the problem! >>> Linda >>> >>>> ------------------------------ >>>> >>>> Message: 25 >>>> Date: Fri, 10 Aug 2012 11:18:38 -0400 >>>> From: Douglas N Greve<greve(a)nmr.mgh.harvard.edu> >>>> Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats >>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>> Message-ID:<5025264E.3030801(a)nmr.mgh.harvard.edu> >>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>> >>>> what are your command lines? >>>> doug >>>> >>>> On 08/09/2012 01:21 PM, Linda Douw wrote: >>>>> Dear Freesurfers, >>>>> >>>>> I'm trying to extract the average waveforms from all 2562 ROIs in an >>>>> annotation constructed using mris_make_face_parcellation with ico4. >>>>> However, I get only 2460 waveforms after doing mri_segstats, and the >>>>> summary files show that several ROIs are 'skipped' for some reason. Am >>>>> I >>>>> missing something? >>>>> >>>>> Thanks, >>>>> -- 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

2 5

T1w3D scan properties of pts with epilepsy
by Zuzana Nedelska 14 Sep '12

14 Sep '12

Hello: I have big file of pts with medial temporal lobe epilepsy (they usually have hippocampal sclerosis, atrophy; sometimes MRI signal changes in amygdala). Pts are scanned with 'oblique' sequence, as it is perpendicular to long axis of hippocampus. Can these oblique sequences be used for FreeSurfer cortical reconstruction and subcort. volumes? I put some of them through 'recon-all' pipeline, which finished 'without errors'. In the 'stats' files (aseg.stats) of those subjects, I am missing volumetric values for left hippocampus and left amygdala. Patients are before surgery, so they have left structures for sure (even original dicom data are complete). The right hipo and amygdala volumes are stated in mm3 as expected. Why is that? Thanks for the advice.

3 2

Numerical result out of range error
by Blessy M 14 Sep '12

14 Sep '12

I have a MPRAGE scan, with slight atrophy on right side of brain. Recon-all is crashing (see error below). Can anyone help me with this, so I can get a reasonably parcellated brain? *CORRECTING DEFECT 6 (vertices=151, convex hull=90) After retessellation of defect 6, euler #=-52 (54998,159712,104662) : difference with theory (-57) = -5 CORRECTING DEFECT 7 (vertices=27939, convex hull=5437) normal vector of length zero at vertex 60965 with 0 faces vertex 60965 has 0 face Numerical result out of range Linux compute-0-4.local 2.6.18-194.17.4.el5 #1 SMP Mon Oct 25 15:50:53 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s . exited with ERRORS at Sat Sep 1 02:01:53 EDT 2012* thanks

2 1

Re: [Freesurfer] ERROR: You are trying to re-run an existing subject
by Douglas N Greve 14 Sep '12

14 Sep '12

And before you run this, does $SUBJECTS_DIR/HPTU_vol11_2012 exist? BTW, try it without a slash at the end of the name. doug On 09/14/2012 02:09 PM, Carolina Valencia wrote: > > Sure! > cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria$ > recon-all -s HPTU_vol11_2012/ -i > HPTU_vol11_2012/dicom/MPRAGE.Ser1.Img0.dcm > > 2012/9/14 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > What is your command line? > doug > > > > On 09/14/2012 12:23 PM, Carolina Valencia wrote: > > Hi Freesurfer users: > > > > I'm trying to run recon-all command in a single subject and > > I don't know why always there is an error message about the names, I > > tried the suggestionsin the message, rename the files, folders, > > eliminate the folders etc > > But I don't succeed to star to running my data. > > Many thanks, > > > > > > ERROR: You are trying to re-run an existing subject with (possibly) > > new input data (-i). If this is truly new input data, you > should delete > > the subject folder and re-run, or specify a different subject name. > > If you are just continuing an analysis of an existing subject, then > > omit all -i flags. > > > > -- > > -- > > *Carolina Valencia Muñoz* > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <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> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

Two questions about csd (cluster simulation data)
by Shanqing Cai 14 Sep '12

14 Sep '12

Hi, These might be old questions, but I couldn't find any entries related to them in the archives. 1) In the surface and volume csd files, what are the units of the "maxclustsize" columns? Are they mm^2 and mm^3 for surface and volume, respectively? Or are the voxel / vertex counts? 2) When mri_surfcluster uses a csd file to compute the cluster-wise correct p-values, how does it do that? Does it only use the maxclustsize? Or does it take other columns, such as maxsig, into account as well? Thanks! Best, Shanqing Cai

2 1

ERROR: You are trying to re-run an existing subject
by Carolina Valencia 14 Sep '12

14 Sep '12

Hi Freesurfer users: I'm trying to run recon-all command in a single subject and I don't know why always there is an error message about the names, I tried the suggestionsin the message, rename the files, folders, eliminate the folders etc But I don't succeed to star to running my data. Many thanks, ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. -- -- *Carolina Valencia Muñoz*

2 1

recon-all problem
by Eiran Vadim Harel 14 Sep '12

14 Sep '12

Hi all, Is there a change in the unpacking of the MPRAGE and DICOM files? The names of the files have changed. what file name should be put in the command: recon-all -i./file name -s subjectname Thanks, Eiran

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Freesurfer September 2012