The error is: "Mapping unhit to unknown. Found 137851 unhit vertices". The file is made, but when trying to select it from the annotation tab in Freeview, Freeview crashes too.
Regards, Caroline -----Oorspronkelijk bericht----- Van: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens freesurfer-requ...@nmr.mgh.harvard.edu Verzonden: donderdag 11 augustus 2016 18:00 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Freesurfer Digest, Vol 150, Issue 14 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. aseg.stats data output (shi yao wang) 2. mri_glmfit-sim problem (miracle ozzoude) 3. Re: mri_glmfit-sim problem (miracle ozzoude) 4. Re: Registration of low-resolution EPI time series to CVS MNI (avoiding resampling) (Douglas N Greve) 5. Re: resample structural ROI in functional space? (Douglas N Greve) 6. Re: query about the "normal range" in aseg.stats (Douglas N Greve) 7. Re: aseg.stats data output (Douglas N Greve) 8. Re: Problems with QDEC (Douglas N Greve) 9. Re: group analysis/ region of interest (ROI) approach (Douglas N Greve) 10. Re: Inquiries about QDEC inflated surface (Douglas N Greve) 11. Re: FS V6.0 GTM PVC ROI definition (Douglas N Greve) 12. Re: Fw: Running recon-all with T1 and FLAIR (Douglas N Greve) 13. Re: myaparc (Douglas N Greve) 14. Re: Qdec Generate Stats Data Table Error (Douglas N Greve) 15. Re: bbregister problem in FS5.1 (Douglas N Greve) 16. Re: Error with qdec (Douglas N Greve) 17. Re: Assessing local correlations across 2 modalities (Douglas N Greve) 18. Re: FS V6.0 GTM PVC ROI definition (Pradeep) 19. Re: FS V6.0 GTM PVC ROI definition (Douglas N Greve) 20. Re: Retinotopy questions (Douglas N Greve) 21. how to run correlation analysis between cortical thickness and cognitive function (Liu Y) 22. Re: how to run correlation analysis between cortical thickness and cognitive function (Douglas N Greve) ---------------------------------------------------------------------- Message: 1 Date: Wed, 10 Aug 2016 12:38:45 -0400 From: shi yao wang <wangshiyao2...@gmail.com> Subject: [Freesurfer] aseg.stats data output To: freesurfer@nmr.mgh.harvard.edu Message-ID: <CA+rJNW_0aSv=AtUCFtKM=bv_7iqzzl+agfac-wwct5veaxr...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear FS experts: How can I only out put the volume value in the aseg.stats file? I applied following command: but it will produce a table with lots of values such as brainsegvol, brainsegvolnotvent, which I donot want to use. thanks asegstats2table --subjects 004 021 040 067 080 092 \ --segno 11 17 18 \ --tablefile aseg.vol.table -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160810/51159869/attachment-0001.html ------------------------------ Message: 2 Date: Wed, 10 Aug 2016 12:50:47 -0400 From: miracle ozzoude <miracoo...@gmail.com> Subject: [Freesurfer] mri_glmfit-sim problem To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu> Message-ID: <CANfOk0hWx6X=H5z4CWHHDn66HhrnauerKzMgJP5jFUtvNz1W=q...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello FreeSurfer experts, I am running surfaced based analysis using ROI approach. My mris_preproc, mri_surf2surf and mri_glmfit worked as expected. Since i restricted the region i built my own monte carlo "mri_mcsim --o roianalysis/average/mult-comp-cor/fsaverage/rh/rightmaskforcomp --base mc-z --surface fsaverage rh --nreps 10000 --label 2mask" which worked. However, when I wanted to run the mri_glmfit-sim using this command line " mri-glmfit-sim --glmdir rh.score.glmdir --cache-dir roianalysis/average/mult-comp-cor --cache-label rightmaskforcomp --cache 2 pos --cwpvalthresh 0.05 --2spaces" i got an error "setenv SUBJECTS_DIR users/paul/desktop/roianalysis FREESURFER_HOME/ applications/freesurfer original mri_glmfit command line ............ DoSim = 0 UseCache = 1 dopoll = 1 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 17.292581 ERROR: cannot find roianalysis/average/mult-comp-cor/fsaverage/rh/rightmaskforcomp/fwhm17/pos/th20/mc.z.csd" I looked into roianalysis/........./fwhm17/pos/th20/mc.z.csd and it does exist. I saw a post like this on the forum but it wasn't answered. How can I direct it to my simulation on my subjectfolder (i.e., desktop/roianalysis/......)? Thanks Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160810/e440f882/attachment-0001.html ------------------------------ Message: 3 Date: Wed, 10 Aug 2016 13:22:31 -0400 From: miracle ozzoude <miracoo...@gmail.com> Subject: Re: [Freesurfer] mri_glmfit-sim problem To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu> Message-ID: <canfok0j+mxhhfbjywvxf13r4oo1lizhvkvvm40fisqhknzg...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, Never mind. I was able to figure it out. I only needed to add "Users/Paul/Desktop" to the command line On Wed, Aug 10, 2016 at 12:50 PM, miracle ozzoude <miracoo...@gmail.com> wrote: > Hello FreeSurfer experts, > I am running surfaced based analysis using ROI approach. My mris_preproc, > mri_surf2surf and mri_glmfit worked as expected. Since i restricted the > region i built my own monte carlo "mri_mcsim --o > roianalysis/average/mult-comp-cor/fsaverage/rh/rightmaskforcomp --base > mc-z --surface fsaverage rh --nreps 10000 --label 2mask" which worked. > However, when I wanted to run the mri_glmfit-sim using this command line " > mri-glmfit-sim --glmdir rh.score.glmdir --cache-dir > roianalysis/average/mult-comp-cor --cache-label rightmaskforcomp --cache > 2 pos --cwpvalthresh 0.05 --2spaces" i got an error > > "setenv SUBJECTS_DIR users/paul/desktop/roianalysis > FREESURFER_HOME/ applications/freesurfer > original mri_glmfit command line ............ > > DoSim = 0 > UseCache = 1 > dopoll = 1 > DoPBSubmit = 0 > DoBackground = 0 > DiagCluster = 0 > gd2mtx = dods > fwhm = 17.292581 > ERROR: cannot find roianalysis/average/mult-comp-cor/fsaverage/rh/ > rightmaskforcomp/fwhm17/pos/th20/mc.z.csd" > > I looked into roianalysis/........./fwhm17/pos/th20/mc.z.csd and it does > exist. > I saw a post like this on the forum but it wasn't answered. How can I > direct it to my simulation on my subjectfolder (i.e., > desktop/roianalysis/......)? Thanks > Paul > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160810/5a33b210/attachment-0001.html ------------------------------ Message: 4 Date: Wed, 10 Aug 2016 17:25:44 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Registration of low-resolution EPI time series to CVS MNI (avoiding resampling) To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57ab9bd8.6040...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed first, you'll need to get two new things: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cvs152.mri2.mm.tar.gz ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol cd $FREESURFER_HOME/subjects/cvs_avg35_inMNI152 tar xvfz cvs152.mri2.mm.tar.gz # Make a backup of mri_vol2vol, then cp mri_vol2vol$FREESURFER_HOME/bin Now, run mri_vol2vol like this mri_vol2vol --gcam EPI.nii.gz reg.lta $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 output.nii.gz where reg.lta is the output of bbregister (don't use the EPI.nii.gz that has been changed with --no-resample) This will create an output with 2mm voxel size. If you really want to do 3mm, then you can try creating your own mri.3mm subdir like the mri.2mm subdir you just added. On 08/05/2016 08:02 AM, Heidi Grohn wrote: > > Hi Freesurfer (FS) users, > > I am a new user in the world of FS and I am trying to normalize rsfMRI > EPI series to CVS MNI space. I would like to do it without resampling > the EPI images to 1*1*1mm3 resolution. > > I've registered EPI series to FS T1 space by using following command > (after bbregister), with --no-resample flag, after which the > resolution of the EPI images did not change. > > mri_vol2vol --mov EPI.nii.gz --targ ...subject/mri/wmparc.mgz --interp > trilinear --o EPI_in_FS_T1_space.mgz --reg EPI_in_FS_T1_space.dat > --no-resample --no-save-reg > > After that I used the following command to apply normalization to CVS > MNI, but I cannot find any similar option to maintain the low > resolution. Output is always on 1*1*1mm3 resolution. > > applyMorph --template ../cvs_avg35_inMNI152/mri/norm.mgz --transform > ..subject/cvs_mni/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d > \vol EPI_in_FS_T1_space.mgz EPI_in_MNI.mgz trilinear > > In summary, how would I maintain the resolution of the EPI images > after normalization? By the way, I am using Freesurfer 5.3. > > Your help is very much appreciated, Thanks, > > Heidi > > %%%%%%%%%%%%%%%% > > Heidi Gr?hn, PhD > > CMRR > > University of Minnesota > > %%%%%%%%%%%%%%%% > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 5 Date: Wed, 10 Aug 2016 17:29:56 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] resample structural ROI in functional space? To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57ab9cd4.9080...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Use mri_label2vol On 08/08/2016 02:33 PM, Kami Koldewyn wrote: > Hi All, > > I have a set of ROIs that were created in structural space, currently > saved as volume masks. I would like to transform these into functional > space, re-sampled to the functional resolution. Can anyone suggest a > good way to do this? > > > -kami > > *Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565* > > Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, > gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig > gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y > neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith > a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i > chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir > ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn > unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid > yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw > atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn > wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y > neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr > awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. > > This email and any attachments may contain confidential material and > is solely for the use of the intended recipient(s). If you have > received this email in error, please notify the sender immediately and > delete this email. If you are not the intended recipient(s), you must > not use, retain or disclose any information contained in this email. > Any views or opinions are solely those of the sender and do not > necessarily represent those of Bangor University. Bangor University > does not guarantee that this email or any attachments are free from > viruses or 100% secure. Unless expressly stated in the body of the > text of the email, this email is not intended to form a binding > contract - a list of authorised signatories is available from the > Bangor University Finance Office. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 6 Date: Wed, 10 Aug 2016 17:33:24 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] query about the "normal range" in aseg.stats To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57ab9da4.20...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed It says "normRange" not "normalRange" "norm" refers to the fact that the norm.mgz was used to generate the values. It has nothing to do with normal range of human values On 08/10/2016 11:41 AM, shi yao wang wrote: > Dear FS experts: > I noticed that there is a "normal Range" results in the aseg.stats table. > I am wondering how can I consider of this normal range? is that based > on population or what. > > thanks > Lawrence > > Emory University > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 7 Date: Wed, 10 Aug 2016 17:35:24 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] aseg.stats data output To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57ab9e1c.6070...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed With the version 5.3 asegstats2table, you will always get these. In version 6, you'll have the opportunity to get only the segs you specify. On 08/10/2016 12:38 PM, shi yao wang wrote: > Dear FS experts: > How can I only out put the volume value in the aseg.stats file? > > I applied following command: but it will produce a table with lots of > values such as brainsegvol, brainsegvolnotvent, which I donot want to > use. > > thanks > asegstats2table --subjects 004 021 040 067 080 092 \ > --segno 11 17 18 \ > --tablefile aseg.vol.table > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 8 Date: Wed, 10 Aug 2016 17:47:03 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Problems with QDEC To: Vikas Bandalli <vikasb...@gmail.com>, "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu> Message-ID: <57aba0d7.5000...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed 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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 gr...@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/ ------------------------------ Message: 9 Date: Wed, 10 Aug 2016 17:49:00 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] group analysis/ region of interest (ROI) approach To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57aba14c.6010...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed On 08/05/2016 02:35 PM, miracoo...@gmail.com wrote: > Hello doug, > Should I add --label-src in addition to --label-trg or should I replace the > latter with the former? It does not matter as both the source and target are fsaveage > Thanks. Also, Just to conform, I should run mri_glmfit-sim after mri_mcsim. correct > Best, > Paul > > Sent from my BlackBerry 10 smartphone. > Original Message > From: Douglas N Greve > Sent: Friday, August 5, 2016 11:49 AM > To: freesurfer@nmr.mgh.harvard.edu > Reply To: Freesurfer support list > Subject: Re: [Freesurfer] group analysis/ region of interest (ROI) approach > > There are several things that need to be changed as I've indicated below > > On 08/01/2016 10:09 PM, miracle ozzoude wrote: >> Thanks doug. Also, Please can you verify if this are the right codes >> for performing ROI surface based analysis using the command line. I >> tried to reverse the whole brain analysis tutorial with some of the >> previous threads i read. I'm trying to mask the entorhinal and MT and >> then perform ROI on them using GLM. Thanks a lot >> >> CREATE MASK USING MRI_BINARIZE >> setenv SUJECTS_DIR users/paul/desktop/ims/fsaverage/mri >> cd users/paul/desktop/ims/fsaverage/mri >> mri_binarize --match [subjects] -i aparc+aseg.mgz -o lh.2mask.mgz >> >> MERGE TO LABELS >> cd users/paul/desktop/ims/fsaverage/label >> mri_mergelabels -i lh.entorhinal.label -i lh.MT.label -o lh.2mask.label >> >> MRIS_PREPROC >> cd users/paul/desktop/ims >> mris_preproc -fsgd filename.fsgd --target fsaverage hemi lh --meas >> thickness --out lh.filename.thickness.00.mgh >> >> MRI_SURF2SURF >> mri_surf2surf --hemi lh --s fsaverage --sval >> lh.filename.thickness.00.mgh --fwhm 10 --label-trg >> fsaverage/label/lh.2mask.label --tval lh.filename.thickness.10B.mgh > Add --label-src lh.2mask.label > This will cause it to smooth only in the mask >> GLM >> mri_glmfit --y lh.filename.thickness.10B.mgh --fsgd filname.fsgd dods >> --C contrastmatrix.mtx --surf fsaverage lh --label >> fsaverage/label/lh.2mask.label --glmdir lh.filename.glmdir >> >> CORRECTING FOR MULTIPLE COMPARISONS WITH MONTE CARLO 5000 iterations >> mri_glmfit-sim --glmdir lh.firstscore.glmdir --sim mc-z 5 2 >> mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --2spaces > You will need to create your own correction simulation since you have > changed the search space. See here > http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo >> On Mon, Aug 1, 2016 at 9:50 PM, Douglas Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> I think there is an example on the wiki in the ROI analysis >> section. See >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI >> >> After you run aparcstats2table, you can run mri_glmfit with >> --table aparcstatstable instead of --y. The output folder will >> have tables with lists of ROIs and p-values >> >> >> >> On 7/30/16 5:33 PM, miracle ozzoude wrote: >>> 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 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> 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. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 10 Date: Wed, 10 Aug 2016 17:50:09 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Inquiries about QDEC inflated surface To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57aba191.7030...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed I don't know what you mean. Can you elaborate? On 08/05/2016 04:10 PM, Mahtab Farahbakhsh wrote: > 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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 11 Date: Wed, 10 Aug 2016 17:55:02 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FS V6.0 GTM PVC ROI definition To: Pradeep <tprad...@gmail.com>, "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu> Message-ID: <57aba2b6.2010...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed 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 <tprad...@gmail.com > <mailto:tprad...@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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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@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 gr...@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/ ------------------------------ Message: 12 Date: Wed, 10 Aug 2016 17:56:47 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57aba31f.5080...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed did you look at the aseg.mgz to see if the lesions were in the right place? On 08/10/2016 03:28 AM, Silas wrote: > > Thank you very much for your help Douglas! > > > I had a few problems running these commands. > > 1) recon-all -autorecon1 -autorecon2 -> no problems > > > 2) The matlab script > > The aseg.auto.mgz (256x256x256) didn't have the same size as the FLAIR > (resliced to 1mm, co-registered in MNI-space and with manually drawn > binary lesion masks (218x182x182)). I overcome this problem by > reslicing the FLAIR image and using aseg.auto.nii as the image > defining space. This was done in SPM8, and prior to this the > aseg.auto.mgz was converted to a .nii using mri_convert. > > This seemed to solve the problem! > > > 3) recon- all -autorecon2-cp -autorecon3 > > When running the following command i get this error: > > /depot64/freesurfer/freesurfer.5.3.0/bin/recon-all -s 01MS > -autorecon2-cp -autorecon3 subjid 01MS > > ............ > > > '#@# Intensity Normalization2 Mon Aug DATE > /.../subjects_FLAIR/01MS/mri > > mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz > > using segmentation for initial intensity normalization > using MR volume brainmask.mgz to mask input volume... > reading from norm.mgz... > Reading aseg aseg.mgz > normalizing image... > processing with aseg > removing outliers in the aseg WM... > 5361 control points removed > Building bias image > mriMarkUnmarkedNeighbors: all inputs must be MRI_UCHAR or MRI_INT > building Voronoi diagram... > Numerical argument out of domain > Linux big28 3.13.0-66-generic #108-Ubuntu SMP Wed Oct 7 15:20:27 UTC > 2015 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s 01MS exited with ERRORS at Mon Aug 8 15:31:32 CEST 2016 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting' > > *How can i solve this problem?* > > > Best, Silas > > > > ------------------------------------------------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve > <gr...@nmr.mgh.harvard.edu> > *Sent:* Tuesday, August 2, 2016 4:06 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR > > That recon-all command will not work as the FLAIR input should be a > simple FLAIR image. The FLAIR will only correct the pial surface and > will have nothing to do with lesion segmentation. Emily Lindermer has > a tool that can take a T1 and FLAIR and produce a lesion map; but > given that you already have manual segmentations, maybe that is not so > helpful. One thing you can do is to edit the aseg.mgz to insert your > lesions. First run recon-all with -autorecon1 -autorecon2 instead of > -all. Then, in matlab, > > > aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg > > manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever > format, but should be binary > > ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol != 0); > > newaseg = aseg; > > newaseg.vol(ind) = 77; > > MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so > make a backup > > > Then run recon-all with -autorecon2-cp -autorecon3 > > > > On 8/1/16 7:35 AM, Silas wrote: >> >> >> Dear FreeSurfer team, >> >> >> I'm doing a structural analysis with 50 MS patients and 50 healthy >> controls (T1, T2 and FLAIR). The MS patients have multiple lesions >> mainly in white matter. My co-worker did manual editing (bullet >> points) in the FLAIR images, and i would like to use these edits when >> running recon-all in order to avoid further manual editing. >> >> >> The data i'm working with is already resliced to 1 mm and >> co-registered in MNI-space. >> >> 1) Can i use this data or would it be preferable to use the original >> T1's? >> >> >> My thought was to run the following command: >> >> recon-all -subject subjectname -i /path/to/input_volume -FLAIR >> /path/to/FLAIR_volume_with_edits-FLAIRpial -all >> 2) Does this look correct? Is there anything i should be aware of? -> >> update: Does this command only improve the pial surface? How can i >> also improve the white mater segmentation (white) using FLAIR >> corrections? >> >> 3) Does it make a difference running recon-all -all with the FLAIR >> image - compared to running recon-all -autorecon3 with the FLAIR >> after running recon-all -all with only the T1? >> >> 4) I've also thought about using the lesion segmentation toolbox for >> SPM and completely avoid manual editing - is this preferable to using >> the FLAIR with manual editing? >> >> 5) How is the general strength of analysing corpus callosum >> structurally in MS patients using FreeSurfer? >> >> >> Best, Silas >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 13 Date: Wed, 10 Aug 2016 17:57:31 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] myaparc To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57aba34b.7030...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed what is the error? On 08/10/2016 04:45 AM, Caroline Beelen wrote: > > 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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > Subject: Re: [Freesurfer] mapping error > > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > Message-ID: <f3f77469-16ad-6fdf-f647-80aee162d...@nmr.mgh.harvard.edu > <mailto:f3f77469-16ad-6fdf-f647-80aee162d...@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: > > > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 14 Date: Wed, 10 Aug 2016 17:59:22 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Qdec Generate Stats Data Table Error To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57aba3ba.9010...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed did you look at the file it points to as the source of the error? /local/limachiagv/freesurfer/subjects/CON_201/stats/aseg.stats On 07/27/2016 05:00 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote: > 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 15 Date: Wed, 10 Aug 2016 18:01:37 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] bbregister problem in FS5.1 To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57aba441.4070...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed I have no idea. You can try copying the 5.3 version of mri_segreg to 5.1 On 07/28/2016 04:10 AM, Fred Sampedro wrote: > Hi Douglas, > > > Thanks a lot for your help, I understand. I tried replacing the > mri_convert in 5.1 from the 5.3 and the bbregister command went a > little bit further. Unfortunately, it segfaulted again when computing > the relative costs. > > I'm attaching the output of the same command in 5.3 and in 5.1. Until > the "Loading mov" in line 210, the output is actually the same. Could > it be related to errors regarding the reading of the PET image? > > If anyone could help me figuring out which instruction is failing so I > could try to replace it with the 5.3 version I would be very grateful. > > Thanks a lot in advance, > > Fred > > On Tue, Jul 26, 2016 at 1:30 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Sorry, I have no idea and I'm not going to try to dig in to 5.1 to > see. You can just copy mri_convert from 5.3 into 5.1 (make a > backup first) > > > On 7/25/16 12:31 PM, Fred Sampedro wrote: >> Hi Douglas, >> >> Thank you very much for answering. Unfortunately, I can read all >> the files without any problem in FSL/SPM, and I still have more >> than 40GB of free space. In fact, running the exact same >> instruction in freesurfer 5.3 works fine. >> >> :( >> >> >> >> On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> It looks like one of two things: >> >> 1. The files SUBJ_ID.nii.gz is corrupted. See if another tool >> (FSL, SPM, AFNI) can read the file >> >> 2. You have run out of disk space >> >> >> On 7/24/16 10:52 AM, Fred Sampedro wrote: >>> 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 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> 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. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > 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. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 16 Date: Wed, 10 Aug 2016 18:02:26 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error with qdec To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57aba472.7010...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Try normalizing your continuous variables (ie, subtract the mean and divide by the stddev) On 07/28/2016 06:06 AM, Mahtab Farahbakhsh wrote: > 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. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 17 Date: Wed, 10 Aug 2016 18:04:29 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Assessing local correlations across 2 modalities To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57aba4ed.2040...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed You can use the "per vertex regressor" functionality in mri_glmfit. You create a stack of on of the modalities that you pass with the --pvr flag. This adds the value for each subject as a column in the design matrix. You'll need to create contrast matrices with this extra regressor in mind On 07/27/2016 03:33 PM, Elijah Mak wrote: > 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 18 Date: Wed, 10 Aug 2016 22:06:22 +0000 From: Pradeep <tprad...@gmail.com> Subject: Re: [Freesurfer] FS V6.0 GTM PVC ROI definition To: Douglas N Greve <gr...@nmr.mgh.harvard.edu>, "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu> Message-ID: <CAPxM4Xkye3b4Sbkwpxeu4mVtVWBycfvW=SAC=G-n9Ec3=z_...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Its in PET native space. On Wed, Aug 10, 2016 at 2:55 PM Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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 <tprad...@gmail.com > > <mailto:tprad...@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 > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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@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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@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@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 > gr...@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/ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160810/a3037b30/attachment-0001.html ------------------------------ Message: 19 Date: Wed, 10 Aug 2016 18:08:17 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FS V6.0 GTM PVC ROI definition To: Pradeep <tprad...@gmail.com>, "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu> Message-ID: <57aba5d1.4040...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed Use the pet2bbpet.lta in the aux folder. If you add --no-reduce-fov, it will not change the FoV of the output image On 08/10/2016 06:06 PM, Pradeep wrote: > Its in PET native space. > > On Wed, Aug 10, 2016 at 2:55 PM Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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 <tprad...@gmail.com > <mailto:tprad...@gmail.com> > > <mailto:tprad...@gmail.com <mailto:tprad...@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 > > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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@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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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> > > <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> > > > <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@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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/ > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 20 Date: Wed, 10 Aug 2016 18:10:23 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Retinotopy questions To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57aba64f.5060...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Neither of these are easily fixable in FSFAST. You can remove the extra time points for the first problem. For the 2nd one, I guess you can do two analyses, one at each frequency, then ignore the one with the wrong frequency On 08/02/2016 05:55 PM, Xiaomin Yue wrote: > Hi, > > I am running a retinotopy analysis using fsfast 5.3. The design has > 15 TR blank before and after wedge presented for 30 TR with 7 repeats, > and ring presented for 24 TR with 7 repeats. Here is my analysis: > mkanalysis -s vz -a rtoy.self.rh -fsd bold -fwhm 2 -nskip 15 -TR 1.5 > -retinotopy 48 -paradigm rtopy.par. > > The data doesn't look right. I assume that the analysis does require > the stimuli presentation as a full circle, which means that the last > 15 TR blank was accounted as the stimuli presentation time. If I am > correct, is there simple way to take care of it in mkanalysis-sess? > Second, the ring and wedge were presented in different frequency. It > seems that the anslysis-sess does not take this into account in the > current configration. Is there a way to specify this? > > Thanks very much for the help. > > Xiaomin > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ Message: 21 Date: Thu, 11 Aug 2016 15:23:50 +0300 From: Liu Y <liuy8...@gmail.com> Subject: [Freesurfer] how to run correlation analysis between cortical thickness and cognitive function To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu> Message-ID: <CAFXerOy7CUtEK=yzvdkwskfucxe28fv55hof8dzrtq4bvbx...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Expert, How to run the correlation analysis between cortical thickness and cognitive function with Qdec? Best regards, Yawu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160811/f19c76f4/attachment-0001.html ------------------------------ Message: 22 Date: Thu, 11 Aug 2016 11:20:21 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] how to run correlation analysis between cortical thickness and cognitive function To: freesurfer@nmr.mgh.harvard.edu Message-ID: <57ac97b5.4070...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed see our tutorials on our wiki. Basically, you need to create a qdec dat file with your cognitive covariates or group assignemnts On 08/11/2016 08:23 AM, Liu Y wrote: > Dear Expert, > How to run the correlation analysis between cortical thickness and > cognitive function with Qdec? > Best regards, > Yawu > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 150, Issue 14 ******************************************* _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
