Freesurfer August 2016

freesurfer@nmr.mgh.harvard.edu

127 participants
198 discussions

Inter-rater and intra-rater reliability
by Annemarie Brandhofe 12 Aug '16

12 Aug '16

Dear FreeSurfer experts, I have a question regarding manual interventions during the recon-all script of FreeSurfer 5.3.0 (i.e. setting control points, performing white matter edits). How can we check for inter- and intra-rater reliability? In an earlier post you mentioned an intra- and inter-rater reliability study you did. Could you tell me the name of this publication? Thank you in advance for your help! Best regards, Anne

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Performing GLM within a Mask Specified by Another GLM
by Timothy Hendrickson 11 Aug '16

11 Aug '16

Freesurfer Support, Here is what I would like to do: I have run a GLM on the entire cortex to determine whether there are significant differences in LGI between patients and controls. I then would like run a different GLM just with the clusters outputted from the previous GLM. It would seem that the best thing to do is to set a mask representing the clusters from the first GLM and then run the second GLM on the mask. Is this a reasonable thing to do? What steps/commands would I perform in order to do something like this? Respectfully, -Tim Hendrickson Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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Using other brain template to calculate cortical thickness
by shi yao wang 11 Aug '16

11 Aug '16

Dear Douglas Thank you so much for your reply!! Another question: Can we use other brain template to calculate cortical thickness? If yes, How can I do it. thanks Lawrence

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how to run correlation analysis between cortical thickness and cognitive function
by Liu Y 11 Aug '16

11 Aug '16

Dear Expert, How to run the correlation analysis between cortical thickness and cognitive function with Qdec? Best regards, Yawu

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Re: [Freesurfer] FS V6.0 GTM PVC ROI definition
by Douglas N Greve 10 Aug '16

10 Aug '16

which "native" space? the pet native? the anatomical native? On 08/09/2016 05:46 PM, Pradeep wrote: > Hello Doug, > > The aux/seg.nii image which has all the ROI's defined does not seem to > be in the subject's native space or the CVS template space. > > How do I bring it to the subjects native space? > > Thanks, > Pradeep > > Screenshot from 2016-08-09 14:42:10.png > > On Tue, Jul 19, 2016 at 5:03 PM Pradeep <tpradeep(a)gmail.com > <mailto:tpradeep@gmail.com>> wrote: > > Thanks responding Doug! > > I am interested us using centrum semiovale as reference region. Is > there a way I can save the unsegmented white matter [5001& 5002] > during the gtmseg step or what would be its equivalent label in > the gtm_pvc results table? > > Thanks, > Pradeep > > On Thu, Jul 7, 2016 at 11:20 AM Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > > On 06/20/2016 08:25 PM, Pradeep wrote: > > Hello Freesrufer Team, > > > > I am trying to use the Partial volume correction procedure > implemented > > in the freesurfer 6 beta version and have a few questions. > > > > In your recent Neuroimaging paper, the left and right > hemispheres were > > combined by taking the average of the two as they did not > show any > > age-by-hemisphere interaction. > > > > I might have interpreted the Supplementary figure 1 > incorrectly, but > > the Geometric transfer matrix seem to show around 52 ROI's, > So were > > the L and R ROIs combined for the PVC results you reported > in that > > paper? Or were the same 52 used for the general PVC in the > FS pipeline? > They were combined only after the PVC calculation. For the > figure, I > changed the GTM to show the combined GTM. > > > > Do you have any concrete results to examine the effects of > the size > > variation over the ROIs used for PVC? > Not sure what you mean here. You can get the variance > reduction factor > for each ROI in the gtm.stats.dat file. This indicates how > much noise > reduction you can expect (assuming gaussian noise, etc) in > each ROI > given the size and anatomical distribution of the ROIs and PSF. > > Should a threshold be set for the sizes of these ROIs? > What do you mean? > > > > How were the white matter hypo-intensities dealt with while > generating > > the ROI masks? > I merged them with WM. I tried it with and without, and it did > not make > much of a difference. > doug > > > > > > Thanks, > > Pradeep > > > > > > > > _______________________________________________ > > 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 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Assessing local correlations across 2 modalities
by Elijah Mak 10 Aug '16

10 Aug '16

Dear Freesurfer Community, I am currently trying to investigate the local correlations across 2 modalities (i.e. Tau-PET and cortical thinning). I understand that this sort of questions has been conventionally addressed using the Biological Parametric Mapping (BPM) toolbox in MATLAB. Is there a way in Freesurfer to properly address this? My PET data have already been registered and projected to the surfaces for each individual. Thanks a lot. Best Wishes, Elijah -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Error with qdec
by Mahtab Farahbakhsh 10 Aug '16

10 Aug '16

Dear FreeSurfer, I am trying to compare my subjects to the healthy group, but when I put the matrix into qdec, I get the following error: Normalized matrix condition is 1e+08 Design matrix ------------------ 1.000 0.000 0.000 0.000 68.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 66.000 0.000; 1.000 0.000 0.000 0.000 40.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 35.000 0.000; 1.000 0.000 0.000 0.000 72.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 71.000 0.000; 1.000 0.000 0.000 0.000 22.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 22.000 0.000; 0.000 1.000 0.000 0.000 0.000 20.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 20.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 1. Your command line: mri_glmfit --y /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled --surf fsaverage lh --label /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/fsaverage/label/lh.aparc.label --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor-thickness-age.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-spelling-healthy-Intercept-thickness.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-spelling-healthy-Cor-thickness-age.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-X-gender2-diagnosis_spelling-Intercept-thickness.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-X-gender2-diagnosis_spelling-Cor-thickness-age.mat the table file is also attached to the mail. Would you please kindly guide me with this? Best Regards, Mahtab.

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bbregister problem in FS5.1
by Fred Sampedro 10 Aug '16

10 Aug '16

Dear FS experts, I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm trying to run bbregister to register a AV45-PET image to its corresponding FS processed T1 image. For that, I'm trying to run: bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1 And I keep getting segfaults: Log file is register.dat.log dom jul 24 16:44:19 CEST 2016 $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii Segmentation fault (core dumped) I have tried the same installation and command in two different computers and obtained the same segfault. I have also tried the same pipeline using instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same result. I didn't have this issue using freesurfer 5.3, but I need to use 5.1 for an ongoing project. I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits. Any help would be much appreciated, Thanks a lot in advance, Fred Sampedro

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Qdec Generate Stats Data Table Error
by Limachia, Gaurang (NIH/NINDS) [F] 10 Aug '16

10 Aug '16

Hello All, My table.dat file loaded fine. However, I came across the following error when I was running the Qdec generate stats data table. If you can let me know what I can do to fix the following error I would greatly appreciate it. Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /local/limachiagv/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects CON_201 CON_202 CON_203 CON_204 CON_205 CON_206 CON_207 CON_209 CON_211 CON_212 CON_213 CON_214 CON_215 CON_216 CON_217 CON_218 CON_219 CON_220 CON_221 CON_222 CON_223 CON_225 CON_226 CON_227 CON_228 CON_230 CON_231 CON_232 CON_233 CON_234 CON_235 CON_236 CON_237 CON_239 CON_240 CON_241 CON_242 CON_244 CON_245 CON_246 CON_247 CON_248 CON_249 CON_250 CON_251 CON_252 CON_253 CON_254 CON_255 CON_256 CON_257 CON_258 CON_259 CON_260 PAT_402 PAT_403 PAT_407 PAT_409 PAT_410 PAT_411 PAT_412 PAT_413 PAT_414 PAT_415 PAT_416 PAT_417 PAT_418 PAT_419 PAT_421 PAT_422 PAT_424 PAT_425 PAT_426 PAT_427 PAT_428 PAT_429 PAT_430 PAT_431 PAT_432 PAT_433 PAT_437 PAT_439 PAT_440 SUBJECTS_DIR : /local/limachiagv/freesurfer/subjects Parsing the .stats files ERROR: The stats file /local/limachiagv/freesurfer/subjects/CON_201/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thanks, Gaurang

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myaparc
by Caroline Beelen 10 Aug '16

10 Aug '16

Dear FS, I figured out how to list my ctabe-file (attached). Again, the file myaparc was created but this time I got the following error: Colortable:aparc.annot.ctab Annotname: myaparc Nhitsfile nhits.mgh Nlabels 6 Labeltresh 0 0.00000 Loading freesurfer/fsaverage/surf/lh.orig 1 9345678 fusiform 2 145768794 inferiorparietal 3 79873658 inferiortemporal (etc) Mapping unhit to unknown Found 137851 unhit vertices Writing annot to freesurfer/fsaverage/lh.myaparc.annot What goes wrong? My command line is: mris_label2annot --subject fsaverage --hemi lh --ctab aparc.annot.ctab --annot myaparc --l lh.fusiform.label --l lh.inferiorparietal.label (etc.) --nhits nhits.mgh (I have version 5.3) Thanks for your help, Caroline My command line is: mris_label2annot --subject fsaverage --hemi lh --ctab aparc.annot.ctab --annot myaparc --l lh.fusiform.label --l lh.inferiorparietal.label (etc.) --nhits nhits.mgh (I have version 5.3) Regards, Caroline Message: 3 Date: Wed, 3 Aug 2016 09:30:48 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] mapping error To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <f3f77469-16ad-6fdf-f647-80aee162dbfc(a)nmr.mgh.harvard.edu<mailto:f3f77469-16ad-6fdf-f647-80aee162dbfc@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="windows-1252" what is your command line? On 8/3/16 6:00 AM, Caroline Beelen wrote: > > > >

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Freesurfer August 2016