Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

R: Re: R: Re: bvecs tracula
by stdp82＠virgilio.it 31 Jan '13

31 Jan '13

Hi Anastasia, I'm frustrated because I'm checking to resolve this problem anywhere but the error is the same. Can it depend from interaction between fs and new iMAC version (Mountain Lion)? Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 31-gen-2013 22.53 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: bvecs tracula Hi Stefano - See "Specifying Diffusion Gradient Table" in the tracula tutorial for the correct format: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula a.y On Thu, 31 Jan 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > I attach the bvecs that I'm using. The second is produced in the dmri. > You are noting that the first is in 3 rows, the second contains only 3 row with a 0 > > This is the last error > fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 1 > fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz -Tmean > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz > bet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -m -f 0.3 > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mask.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff > #------------------------------------- > #@# Inter-subject registration Gio 31 Gen 2013 22:40:26 CET > flirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -ref > /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni.nii.gz -omat > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat -cost mutualinfo > convert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/mni2diff.mat -inverse > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat > #------------------------------------- > #@# Masks Gio 31 Gen 2013 22:41:55 CET > #------------------------------------- > #@# Tensor fit Gio 31 Gen 2013 22:41:55 CET > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit > Error: bvecs and bvals don't have the same number of entries > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 > x86_64 > > trac-preproc exited with ERRORS at Gio 31 Gen 2013 22:42:02 CET > > Thanks, > > > Stefano > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 31-gen-2013 21.43 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] bvecs tracula > > > Hi Stefano - Are the original bvecs (that you specify in your > configuration file) arranged in 3 rows or 3 columns? > > a.y > > On Thu, 31 Jan 2013, stdp82(a)virgilio.it wrote: > > > Hi list, > > I'm running trac-all -prep -c > > > > but I have this error > > > > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit > > Error: bvecs and bvals don't have the same number of entries > > > > I'm noting that my original bvecs are > > > > 0 -0.460 -0.539 0.490 -0.071 0.226 0.463 0.483 -0.643 0.468 -0.730 -0.707 -0.318 0.175 0.488 0.460 > > 0 -0.395 -0.588 -0.706 -0.605 -0.607 -0.236 -0.180 -0.464 -0.562 -0.337 -0.699 -0.786 -0.786 -0.712 -0.301 > > 0 -0.795 0.419 -0.057 -0.793 -0.725 -0.708 -0.695 -0.609 0.333 0.413 -0.108 0.368 0.392 -0.004 0.476 > > > > and in dmri > > > > 0 > > 0 > > 0 > > > > bvals conversion is ok. What's happen? Why are there an error about conversion to FSL format? > > > > Thank you very much, I really appreciate your patience. > > > > Stefano > > > > > >_______________________________________________ > 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 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.

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R: Re: bvecs tracula
by stdp82＠virgilio.it 31 Jan '13

31 Jan '13

Hi Anastasia, I attach the bvecs that I'm using. The second is produced in the dmri.You are noting that the first is in 3 rows, the second contains only 3 row with a 0 This is the last errorfslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 1fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz -Tmean /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gzbet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -m -f 0.3mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mask.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff#-------------------------------------#@# Inter-subject registration Gio 31 Gen 2013 22:40:26 CETflirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni.nii.gz -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat -cost mutualinfoconvert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/mni2diff.mat -inverse /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat#-------------------------------------#@# Masks Gio 31 Gen 2013 22:41:55 CET#-------------------------------------#@# Tensor fit Gio 31 Gen 2013 22:41:55 CETdtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifitError: bvecs and bvals don't have the same number of entriesDarwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Gio 31 Gen 2013 22:42:02 CET Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 31-gen-2013 21.43 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] bvecs tracula Hi Stefano - Are the original bvecs (that you specify in your configuration file) arranged in 3 rows or 3 columns? a.y On Thu, 31 Jan 2013, stdp82(a)virgilio.it wrote: > Hi list, > I'm running trac-all -prep -c > > but I have this error > > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit > Error: bvecs and bvals don't have the same number of entries > > I'm noting that my original bvecs are > > 0 -0.460 -0.539 0.490 -0.071 0.226 0.463 0.483 -0.643 0.468 -0.730 -0.707 -0.318 0.175 0.488 0.460 > 0 -0.395 -0.588 -0.706 -0.605 -0.607 -0.236 -0.180 -0.464 -0.562 -0.337 -0.699 -0.786 -0.786 -0.712 -0.301 > 0 -0.795 0.419 -0.057 -0.793 -0.725 -0.708 -0.695 -0.609 0.333 0.413 -0.108 0.368 0.392 -0.004 0.476 > > and in dmri > > 0 > 0 > 0 > > bvals conversion is ok. What's happen? Why are there an error about conversion to FSL format? > > Thank you very much, I really appreciate your patience. > > Stefano > > >_______________________________________________ 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.

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bvecs tracula
by stdp82＠virgilio.it 31 Jan '13

31 Jan '13

Hi list, I'm running trac-all -prep -c but I have this error dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifitError: bvecs and bvals don't have the same number of entries I'm noting that my original bvecs are 0 -0.460 -0.539 0.490 -0.071 0.226 0.463 0.483 -0.643 0.468 -0.730 -0.707 -0.318 0.175 0.488 0.4600 -0.395 -0.588 -0.706 -0.605 -0.607 -0.236 -0.180 -0.464 -0.562 -0.337 -0.699 -0.786 -0.786 -0.712 -0.3010 -0.795 0.419 -0.057 -0.793 -0.725 -0.708 -0.695 -0.609 0.333 0.413 -0.108 0.368 0.392 -0.004 0.476 and in dmri 000 bvals conversion is ok. What's happen? Why are there an error about conversion to FSL format? Thank you very much, I really appreciate your patience. Stefano

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slice timing correction and motion correction order
by Maryam Vaziri Pashkam 31 Jan '13

31 Jan '13

Hi Doug, Two questions: 1) In fsfast preprocessing is STC done first or MC? is there a way to control the order? 2) Also if STC is not mentioned in the analysis line and only done in the preprocessing would the analysis be run on the STC data automatically? or should I specify STC in the analysis for the selxavg3-sess to use the stc corrected data? Thanks, M

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Re: [Freesurfer] mean cortical thickness of significant clusters in qdec
by Douglas N Greve 31 Jan '13

31 Jan '13

The threshold must be in the form of -log10(pthreshold). So, if you want pthreshold=.05, then use 1.3 doug On 01/31/2013 07:37 AM, Richter, Julia wrote: > Dear Doug, > > thanks for your reply. I tried the command you suggested, but I always get an error message that there is something wrong with my threshold. I took a screenshot of the command window and attached it to this mail. I will be very happy if you have a look at it. > > Looking forward to your answer, > > Best, Julia > > -----Ursprüngliche Nachricht----- > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve > Gesendet: Mittwoch, 30. Januar 2013 17:16 > An: Richter, Julia; free surfer > Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in qdec > > Oh, sorry, I thought you said you were using mri_glmfit-sim (which does not have an FDR option). Are you using the FDR in QDEC? If so, it will display the voxel-wise threshold that realizes the FDR threshold. You can then run mri_glmfit-sim --cache threshold sign --cwpvalthresh .99 where threshold is the voxelwise threshold from FDR and sign is either abs (absolute), pos, or neg. Setting cwpvalthresh=.99 tell it to report all clusters > > doug > > On 1/30/13 8:09 AM, Richter, Julia wrote: >> No it is not...or I just do not find it. >> >> Might it be that I only get the xxx.y.ocn.dat if I correct for multiple comparisons with Monte Carlo? If yes, is there any possibility that I get this xxx.y.ocn.dat when correcting with FDR? >> >> Many thanks, Julia >> >> -----Ursprüngliche Nachricht----- >> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve >> Gesendet: Dienstag, 29. Januar 2013 18:46 >> An: freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in qdec >> >> Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not? >> doug >> >> >> On 01/29/2013 11:03 AM, Richter, Julia wrote: >>> Dear FreeSurfer experts, >>> >>> I did a group analysis in qdec, found several significant clusters and >>> would now like to extract the mean cortical thickness of each >>> significant cluster. I know that I have to run mri_glmfit-sim to do >>> this, but I do not understand which commands I need to get the >>> xxx.y.ocn.dat as output by running mri_glmfit-sim. >>> >>> Any ideas? Any help is appreciated. J >>> >>> Best wishes, Julia >>> >>> >>> >>> _______________________________________________ >>> 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 >> 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 -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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mri_glmfit-sim output
by Fernando Valle-Inclán 31 Jan '13

31 Jan '13

Hi, Running the mri_glmfit-sim with a threshold set to 20, we get, among other files, cache.th20.pos.sig.cluster.mgh and cache.th20.pos.sig.masked.mgh. Could you explain how to interpret the "masked" file? Thanks

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Re: [Freesurfer] ERROR: aparcstats2table
by Douglas N Greve 31 Jan '13

31 Jan '13

They must be in a single folder and the $SUBJECTS_DIR env variable must be set to that folder. If you know a little unix, you can set up folders with symbolic links to subjects' true directories. doug On 01/23/2013 02:58 PM, Nucleos P wrote: > Thank you for your help Doug! > I was trying to specify the path to get to the subjects. Do I have to > have all the subjects in a folder called 'subjects'? I know the naming > conventions are important. > Thanks again, > Catherine > > On Fri, Jan 18, 2013 at 6:31 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > actually, looking at your cmd line more I see that you have > slashes (/) > in the subject names. The argument to --subjects should just be a list > of name. See the help (aparcstats2table -h) for examples. > doug > > > On 01/18/2013 04:58 PM, Nucleos P wrote: > > Hello experts: > > > > Can someone please help me understand what I am doing wrong? This is > > the first time I am trying this command and it will not work... > > > > COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw > > /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ > /RGS4_31p/rgs1194_raw144/ > > /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t > > RGS4_31p/aparc.volume.rh -m volume --hemi=rh > > > > PATH: > [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd > > /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats > > > > ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects > > Parsing the .stats files > > ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is > > not found or is too small to be a valid statsfile > > Use --skip flag to automatically skip bad stats files > > > > > > Thank you, > > Catherine > > > > > > _______________________________________________ > > 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> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] separate FSAverages and surface-based ROIs
by Douglas N Greve 31 Jan '13

31 Jan '13

Hi Paul, this mostly looks right. I think the problem may be that you are including the unknown label on the command line. I think that mris_label2annot will ignore the 0 inthe ctab file, which means that it assign the first label passed (lh.unknown.label) to the the first non-zero ROI in the ctab file (banksts). Try that and see if it works. doug On 01/30/2013 03:03 PM, Paul Beach wrote: > Hi Doug, > > I've been attempting to utilize the programs suggested by you to > create manual labels (ROIs) on the cortical surface of tksurfer to be > able to export certain ones to AFNI. The problem I was having > originally was that the cortical ribbon was not fully covered by > surface drawn labels that were changed to volumes by MRI_label2vol. > > You suggested first using mri_annotation2label to extract the labels > within the aparc.annot files (left and right hemispheres), putting my > created labels into the same folder (replacing, for example, the > "insula" label with anterior, middle, and posterior insula labels) > and then using mris_label2annotation to make a new annotated file to > be sent into a re-ran mri_aparc2aseg. > > The problem I'm running into now, after extracting all the labels, > putting in my own, and running mris_label2annotis that the resultant > annotation's labels are highly out of place and disorganized. For > example, the label for the cuneus is where the corpus callosum is. > > I'm wondering if this has something to do with the order of labels in > the mris_label2annot script of possibly with my .ctab file. The latter > was created based on what I found here > <https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit> on the > Freesurfer wiki. I simply added my six manual labels/ROIs at the end. > I tried to use their GWFSAnnotToLUT > <https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit?action=AttachF…> program, > but could not get it to work, so I'm not sure if the .ctab file > accurately represents tksurfer's Lookup Table. > > I'm also not sure if it has something to do with overlapping vertices > of different labels. For example, will leaving the "insula" label in > mess things up when I also try to include the anterior, middle, and > posterior insula labels? If so, would simply removing labels that > overlap, vertex-wise, help? > > I have attached the setup of the .ctab file as well as my > mris_label2annot script. > > > Thanks for your advice, > Paul > > > On Tue, Jan 22, 2013 at 2:52 PM, Paul Beach <pabeach1(a)gmail.com > <mailto:pabeach1@gmail.com>> wrote: > > Thanks for your help! > > > > On Tue, Jan 22, 2013 at 11:12 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > mri_annotation2label breaks them appart > mris_label2annot puts them back together again > doug > > On 01/22/2013 11:09 AM, Paul Beach wrote: > > Hi Doug, > > Thank you for this. However, can you give me a hint as to > how I can go about breaking apart the aparc.annot files > into their constituent label files? Are there a particular > commands for doing this and eventually recombining the > labels into the overall aparc.annot file? > > > Thanks! > > > > On Wed, Jan 16, 2013 at 3:15 PM, 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>>> wrote: > > > The "annotation" is the name we give to a surface > segmentation > (eg, lh.aparc.annot). You can break lh.aparc.annot > into its > constituent label files. You can then replace the > insula label > file with posterior and anterior labels that you > create. You can > then recombine the labels back into a new annotation. > Once you > have the new annotation, you can run mri_aparc2aseg to > map the > annotation into the volume. This method will do better > at filling > in the cortical ribbon than mri_surf2vol or mri_label2vol. > > doug > > > > On 01/16/2013 01:25 PM, Paul Beach wrote: > > Hi Doug, > > Thanks a lot for the reply. I'm relatively new to > freesurfer > and it's great to see such a helpful community. > > I'm a little fuzzy on what you mean with your second > suggestion, related to the manual ROI > creation/export to AFNI. > Could you explain a bit more about creating "a new > annotation > and then run mri_aparc2aseg." > > First, I'm not sure what you mean by "new annotation." > > Second, my understanding is that mri_aparc2aseg > normally deals > with ROIs in the LUT. However, looking at the wiki > for this > command, it seems as though I can utilize my > created label > using the "--annot argName" option. > How does this look: > mri_aparc2aseg --s [subj] --annot lh.aIns.label > --o lh.aIns_aparc > > > Cheers, > Paul > > > > On Wed, Jan 16, 2013 at 10:56 AM, 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>>>> wrote: > > Hi Paul, > > On 01/16/2013 10:27 AM, Paul Beach wrote: > > Hello, > > > > I have two issues, currently. > > > > First, I was wondering if it would be > possible to create > separate > > FSAverage brains for different subject > groups. I am > working with > > healthy seniors and various stages of > Alzheimer's > disease, so > doing so > > would be very helpful from the perspective > of not > conflating the > > differences in neuroanatomy between the > these groups. > One idea > we had > > was to create separate HOME directories for > each group, > but we > wanted > > to know if there was an easier way. I can't find > anything in the > > interwebs about this. > You can create your own fsaverage subject using > make_average_subject. > Note that when you run recon-all it registers > to the standard > fsaverage > space. If you want to register to a different > space, you > will need to > re-run mris_register. Once you do this, you > will not be > able to > compare > groups. > > > > Second, I utilize some ROIs that are not > specified by FS > (such as > > secondary somatosensory cortex and anterior > vs. posterior > insula). My > > means of getting around this was to use > FSAverage and > tksurfer to > > hand-draw them, save them as '.label' files, > map them to > individual > > subjects, and export them to AFNI since much > of our > correlation > > analysis is done on that platform. However, > I've noticed > that when I > > view these hand-drawn ROIs in AFNI they only > show up at the > border of > > the gray and white matter, rather than > filling the > entirety of the > > gray matter. Note that this problem does not > occur for > ROIs in the > > look up table (like the caudal ACC). > Exporting these to AFNI > gives you > > a nice ROI that fills all the gray matter in > the defined > region. > Try using --proj frac 0 1 .1 with > mri_label2vol. Or you > can create > a new > annotation and then run mri_aparc2aseg. The > 2nd method > works a little > better since the 1st method can leave some holes. > > doug > > > > _Code I'm using_: > > For the latter problem, what I first use is > mri_label2label to > map the > > fsaverage-based ROI onto individual > subjects, for > example with the > > left anterior insula, before using > mri_label2vol: > > *mri_label2label --srclabel lh.aIns.label > --srcsubject > fsaverage > > --trglabel lh.aIns.label --trgsubject [subj] > --regmethod > surface > > --hemi lh* > > > > *mri_label2vol --label > ../label/lh.aIns.label --regheader > > aparc+aseg.mgz --o gmroi_volume.nii.gz > --temp orig/001.mgz* > > > > > > Then I copy the new volume file to their > AFNI folder, > rename it, and > > run my correlation analysis on them. > > > > Note, that for those ROIs that are in the > look up table > (those > > parcellated by freesurfer) I simply use > mri_label2vol before > > extracting them using 3dcalc (for example, > the caudal > anterior > > cingulate)... > > *mri_label2vol --seg aparc+aseg.mgz --regheader > aparc+aseg.mgz --o > > gmroi_volume.nii.gz --temp orig/001.mgz* > > > > *3dcalc -a gmroi_volume.nii.gz -expr > 'equals(a,1002)' > -prefix > > ROI_FS_lh.caudalACC.nii.gz* > > > > > > > > tl:dr > > Is it possible to "easily" create multiple > FSAverages > based on > > selected subjects (in my case, subject > groups separated by > disease state)? > > > > and > > > > Does anyone have any advice on how to get > hand-drawn > surface-based > > ROIs from Freesurfer's tksurfer into AFNI > that full > cover the > entirety > > of the gray matter? > > > > > > Cheers and thanks! > > -- > > Paul Beach > > > > > > > > _______________________________________________ > > 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> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > > > > -- Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist > Association, MSU COM > Chapter > > > -- 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> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- > Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist Association, MSU > COM Chapter > > > -- > 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> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- > Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist Association, MSU COM Chapter > > > > > -- > Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist Association, MSU COM Chapter -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned
by Ed Gronenschild 31 Jan '13

31 Jan '13

Hi Doug, It is indeed correct that columns 1 and 17 are highly correlated. However, for another version of the fsgd file, where the corresponding class and covariate values where identical but with other covariates (so leading to the same columns 1 and 17, other columns are different), all went well. So probably some other columns are highly correlated as well. Anyway, what can we do about it? Just leave the offending covariate(s) out? Cheers, Ed > Message: 1 > Date: Thu, 24 Jan 2013 12:51:23 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Problem with glmfit: matrix is > ill-conditioned > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <5101749B.4060305(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ed, the problem is that your covariates are highly correlated. Eg, > column 1 is nearly identical to column 17. > doug > > > On 01/24/2013 06:36 AM, Ed Gronenschild wrote: >> Hi, >> >> Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following >> error message: >> >> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >> Possible problem with experimental design: >> Check for duplicate entries and/or lack of range of >> continuous variables within a class. >> If you seek help with this problem, make sure to send: >> 1. Your command line: >> mri_glmfit --y lh.sib_con_cann_aangepast3.thickness.sm0.mgh --fsgd >> ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/fsgd_sib_con_cann_aangepast3.fsgd >> dods --glmdir lh.sib_con_cann_aangepast3.dods.sm0.glmdir --surf >> fsaverage lh --C >> ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/group_thickness_gender_scan_age_educ_hand_cann.mtx >> >> 2. The FSGD file (if using one) >> 3. And the design matrix above >> >> Please find attached the requested files. >> >> I noticed that rows 68 and 147 of the matrix Xg.dat are identical, >> and most probably caused the error. >> In the fsgd file I see that the correspondig cases indeed have >> identical values, although they are referring to different data. >> How to proceed? >> >> Cheers, >> Ed >

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Re: [Freesurfer] beta
by Ed Gronenschild 31 Jan '13

31 Jan '13

Hi Bruce, What do you mean: no support anymore or no new development? Cheers, Ed On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote: > Message: 7 > Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] beta > To: Colin Reveley <reveley(a)gmail.com> > Cc: Joshua Lee <jkilee(a)ucdavis.edu>, freesurfer(a)nmr.mgh.harvard.edu, > Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.00.1301211918340.29285(a)entry.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Colin > > yes, but we simply don't have the person power to do it at the moment. Our > FS support grant ends in a month and is not going to get renewed, so it's > going to be hard to do anytime soon. > > sorry > Bruce

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Freesurfer January 2013