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30135 discussions

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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Inquiries about QDEC inflated surface
by Mahtab Farahbakhsh 10 Aug '16

10 Aug '16

Dear FreeSurfer, I am comparing two groups of my subjects together in qdec and when I want to visualize each subject, I can see two different regions for inferior parietal lobe and supramarginal gyrus. But in the normal pial surface, it seems like that the labels of both overlap with each other. I'm not sure how these two are different. Any guidance would be extremely appreciated. Best Regards, Mahtab.

2 1

group analysis/ region of interest (ROI) approach
by miracle ozzoude 10 Aug '16

10 Aug '16

Hey FreeSurfer experts, Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much. Best, Paul

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Re: [Freesurfer] Problems with QDEC
by Douglas N Greve 10 Aug '16

10 Aug '16

On 08/05/2016 12:33 PM, Vikas Bandalli wrote: > Thank you Doug, > > I am very sorry I hadn't explained our subject considered for analysis. > The subjects group consists of Patients who are classified into > a.Those with Psychosis - Psychotic-pt > b. Those without Psychosis - Non-Psychotic-pt > > We have Age and sex matched controls for every patient (case control > study) > > Now,the study was to see the structural variations using freesurfer > and qdec, > 4 individual 'qdec.dat' files were created such that two groups are > considered at a time and analyzed namely > > *qdec_1.dat :- Normal vs Patients(Psychotic + Non-Psychotic-pt)* > *qdec_2.dat :- Normal vs Psychotic-pt (age and sex matched)* > *qdec_3.dat :- Normal vs Non-Psychotic-pt (age and sex matched)* > *qdec_4.dat :- Psychotic-pt vs Non-Psychotic-pt > * > The design was done as with Diagnosis/Psychosis as fixed factors and > Age as covariate and ICV as nuisance factor for each 'pair' of analysis > > Is the analysis-design appropriately constructed? or is this an > inappropriate method. so you created a new thickness file stack where you subtracted on an individual basis the paired subjects? That is fine. > > The qdec GUI crashed with an error 'matrix m1=null' when the ICV > values were used as it is (demeaning not done) ICV definitely needs to be demeaned (and maybe rescaled by the stddev). > > 1.So,we can retain the negative numbered values for the above design. > Also,I would be very interested to know why demeaning is necessary? > My understanding is that since the ICV values are huge comapared to > other factors Correct > > 2.With the above mentioned study design,I wanted to know if the > structural changes observed is due to the disease per se and not due > to their Lithium intake (Some of the patients {both Psychotic-pt and > Non-Psychotic-pt} were put on lithium). > How would I have to design the analysis then? > Is it possible to analyze this with qdecGUI? To clarify, two diagnosis groups Psychotic Patients and Non-Psychotic Patients. Some of the patients are on lithium and some are not. Is that right? If so, then you have a two factor design where each factor has two levels, so you can do this analysis in QDEC. > > Thank You, > > Regards, > Vikas Bandalli Raju > > On Fri, Aug 5, 2016 at 9:28 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > 1. It is not a problem that some of the demeaned ICV values are > negative; this is what happens when you demean a set of numbers; > you must leave the negative numbers there. Are you doing a paired > analysis or do you just have two groups? I don't think you can do > a paired analysis in QDEC. > > 2. would this give you 3 groups (controls, patients with lithium, > patients without)? If so, you cannot use QDEC for this. > > If you can't use QDEC, you'll have to use the command line stream > and either set up your own FSGD file or your own design matrix > > > On 08/04/2016 01:36 PM, Vikas Bandalli wrote: > > Dear Freesurfers, > > Sorry if the question sounds too basic. > > 1. I am running an analysis on qdec with paired groups - > normal and patients, > To control for IntraCranialVolume(ICV),I am adding it as an > 'nuisance factor',Is it correct? > The suggested mode to add ICV to the tabled was to _demean_ > the ICV. > But when I subtract the mean values from individual subject > ICV values,I noticed that some of the subjects have a negative > demeaned ICV value. > My question is - How should I proceed to include the > data,ignore the negative sign(because I thought a negative ICV > makes no sense) and just keep the values or retain the numbers > with the sign. > Please correct me if I am going wrong in any of the steps. > However,I ran two analysis - one with the sign retained and > other with sign removed ,I noticed that both have very > different results. > > 2. If I want to see the effect due to lithium within the > patient group (Between patients with and without psychosis) > how should I design the matrix in GUI. > I designed the following format > Fixed factor :- Diagnosis - Psychotic-pt > Non-Psychotic-pt > Co-variate :- Lithium use :- 1 - lithium user > 0 - non user > Nuisance factor :- ICV > Is this design correct? > If not how should I construct it ? > Also what query would contain the result for anticipated question > My intention is to control for Diagnosis and then see > effect/change due to lithium use. > > Thank you very much > > > > > -- > Vikas B. R. > Medical student > Bangalore Medical College and Research Institute (BMCRI), > Bangalore,India, > Ph : +918904286825 > > > -- > 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 > <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/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > 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 > <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. > > > > > -- > Vikas B. R. > Medical student > Bangalore Medical College and Research Institute (BMCRI), > Bangalore,India, > Ph : +918904286825 -- 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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