Freesurfer August 2016

freesurfer@nmr.mgh.harvard.edu

127 participants
198 discussions

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.

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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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aseg.stats data output
by shi yao wang 10 Aug '16

10 Aug '16

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

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query about the "normal range" in aseg.stats
by shi yao wang 10 Aug '16

10 Aug '16

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

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resample structural ROI in functional space?
by Kami Koldewyn 10 Aug '16

10 Aug '16

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.

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Registration of low-resolution EPI time series to CVS MNI (avoiding resampling)
by Heidi Grohn 10 Aug '16

10 Aug '16

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 Gröhn, PhD CMRR University of Minnesota %%%%%%%%%%%%%%%%

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mri_glmfit-sim problem
by miracle ozzoude 10 Aug '16

10 Aug '16

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

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white and gray matter masks
by John Anderson 10 Aug '16

10 Aug '16

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New way of installing and running Freesurfer - containers
by Chris Filo Gorgolewski 09 Aug '16

09 Aug '16

Dear all, I have created a Docker image with Freesurfer distribution (and all required dependencies). Features: - Only requires Docker to run (works on Linux, Mac and Windows - does not suffer from the VirtualBox bug <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42474.html> ) - understands BIDS <http://bids.neuroimaging.io/> formatted datasets - performs recon-all on all subjects - allows you to run each subject independently (and potentially in parallel) - automatically performs longitudinal analysis when multiple sessions are detected - creates custom group level template for your study - can be easily converted to a Singularity <http://singularity.lbl.gov/> image using docker2singularity <https://github.com/chrisfilo/docker2singularity> tool and run on your local HPC/cluster You can find more information here: https://github.com/BIDS-Apps/freesurfer Please let me know what do you think! Best, Chris

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Freesurfer August 2016