Re: [Freesurfer] Error first step FS-FAST

001/fmcpr.nii.gz > --mcdat 001/fmcpr.mcdat > > ERROR: cannot find AFNI command 3dvolreg.afni > > > What is 3dvolreg.afni? Where it should be placed? > > > > Thanks in advanced > > > > Stefano > > > > > > ______

Re: [Freesurfer] R: Error first step FS-FAST

3dvolreg.afni? Where it should be placed? > > > > Thanks in advanced > > > > Stefano > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mail

Re: [Freesurfer] R: Error first step FS-FAST

> What is 3dvolreg.afni? Where it should be placed? > > > > Thanks in advanced > > > > Stefano > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvar

Re: [Freesurfer] R: Re: R: Re: R: Error first step FS-FAST

bjects/FUNCTIONAL_DATA/Sess01 > > > > > > RunList: 001 002 003 > > > > > > --- ** --- > > > > > > --- Motion Correcting Run 001 --- > > > > > > --- ** --- > > > > > > sess = Sess01 > > > > > >

Re: [Freesurfer] Possible to generate table of statistics for specific label?

> > Best wishes, > > Sal > > > ___ > 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: s

Re: [Freesurfer] Problem about vol2surf

> > ___ > 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-

Re: [Freesurfer] error unpack dicom

20121214_12.12.14-13_54_00-STD-1.3.12.2.1107.5.2.19.45250_1/fMRI_Aging_Fage_2//Fage_P031b0901030001000100010001.DCM > > /server/data/data14/fwf/FUNC/Fage_P031/bold/02/f2.nii --sdcmlist > /server/data/data14/fwf/FUNC/Fage_P031/bold/02/flf -ot nii > --nspmzeropad 3 --in_type siemens_dicom > > > > ___

Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 131, Issue 13

the lh.BA3a.label file is in the label subfolder for > the individual subject. > > I would like to output the volume, thickness, and area for all the > broadman areas (especially 35). Any advice you can provide on how to > do this would be a great help. > > Thank you for all your

Re: [Freesurfer] fcseed-sess - segmentation fault

gwf.mgh > > Segmentation fault > > > > Thanks in advance, > > > > Stefano > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --

[Freesurfer] Fwd: fcseed-sess - segmentation fault

Having both Thalamus and Thalamus-Proper creates all kinds of confusion. Is there a reason to have both? 9 Left-Thalamus 0 118 14 0 10 Left-Thalamus-Proper0 118 14 0 Forwarded Message Subject:[Freesurfer] fcseed-

Re: [Freesurfer] vol2surf problem

ce > Mapping Source Volume onto Source Subject Surface > 1 0 0 0 > using old > Done mapping volume to surface > Number of source voxels hit = 79447 > Masking with > /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/label/rh.cortex.label > Writing to ./fs_HCP

Re: [Freesurfer] Eccentricity ring start?

panding and contracting runs. Will it affect the analysis? > > Thanks, > > Jack > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf

Re: [Freesurfer] Eccentricity ring start?

btw, it is possible to shift the angle of the eccen when you compute the field sign, but you'll have to run mri_fieldsign directly and not through fieldsign-sess. doug On 01/09/2015 11:42 AM, Douglas N Greve wrote: > The assumption is that it starts at the center/fovea. It will affec

Re: [Freesurfer] Error Message

-- > > > > > > > > > > > > Message: 5 > > > > > > Date: Mon, 5 Jan 2015 09:52:58 +0100 > > > > > > From: maaike rive > > > > > > Subject: [Freesurfer] Extracting vertexvalues >

Re: [Freesurfer] selxavg3-sess

--- > > --- matlab output > > matlab: Command not found. > > -- > > ERROR: fast_selxavg3() failed\n > > > > Thanks in advance, > > > Regards > > > > Stefano > > > > __________

Re: [Freesurfer] Error Message

> > > > > > -subject/media/sf_Dataset/ADHD200/adhd_200/Brown_26001/Brown_26001_1/scans/anat_1-a > > > > > > > > > nat/resources/NIfTI/files/Processed/ -all > > > > > > > > > > > > > > > > > > ? > > > &

Re: [Freesurfer] mask volume with mri_segstats

s correct? Also, is there a way to write out the number of voxels > in the mask with mri_segstats? > > Thanks, > Eunice > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/lis

Re: [Freesurfer] mask volume with mri_segstats

: > Hi Doug- I uploaded an example mask. According to fslstats it has > 29016 voxels whereas mri_segstats suggests it has 26182 voxels. > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=6sthhn0ld2p > > Thanks! > Eunice > > On Jan 12, 2015, at 8:19 AM, Douglas N Greve wro

Re: [Freesurfer] functional connectivity analysis

ge lh > --glmdir my-glm.wls --nii.gz --fsgd group1.fsgd --C group.diff.mtx > --C group1.mtx --C g1g2.intercept.mtx > > Is it corrected? > > 9. Multiple correction > > > ___ > Freesurfer mailing list > Freesurfer@nmr.m

Re: [Freesurfer] qdec group analysis error

gt; more than two levels in a factor. > Is this still the case? > > If this is not possible, can you suggest a freesurfer processing stream that > might suit this type of analysis? > > Thank you! > Gabriella > > > > ___ >

Re: [Freesurfer] Viewing QDEC results in tksurfer

__ > 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/B

Re: [Freesurfer] FREESURFER] ERROR: matrix is ill-conditioned or badly scaled, condno = 164365

A. LEE > > > _______ > 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

Re: [Freesurfer] Apply alignment transformation to a surface?

polis, MN 55455, 612-626-4948 > gran0...@umn.edu <mailto:gran0...@umn.edu> > umn.edu/~gran0260 <http://umn.edu/%7Egran0260> > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.

Re: [Freesurfer] incomplete preprocessing

accidently shut down during the process. > > Thank you. > > Best Regards > > Naveed > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listin

Re: [Freesurfer] Viewing QDEC results in tksurfer

possible? > > Thanks, > > Amanda > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas N Greve > > Sent: 14 January 2015 23:46 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Viewing QDEC res

Re: [Freesurfer] Convert volume index to vertex number in surface

t;> Meiling >> >> >> >> >> >> >> >> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, P

Re: [Freesurfer] Viewing QDEC results in tksurfer

mably this is because all of the T1/orig are stored in each subjects > data file and I'm not trying to look at a specific subject. Is there a way to > get around this problem? > > Best wishes, > > Amanda > > ________ > From: fre

Re: [Freesurfer] Freesurfer Calculation of Vertex-Wise Area

s >> 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 do

Re: [Freesurfer] converting .nii to .mgz

ee the log file >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> Thanks so much, >> Mia >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >

Re: [Freesurfer] Viewing QDEC results in tksurfer

; >>> I'm now having a problem with visualising this with tksurfer, getting >>> ERROR: could not read header info from T1 or orig in >>> /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri >>> >>> Presumably this is because all of

Re: [Freesurfer] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model

rsity *|* 1280 Main Street West, PC329 Psychology > Building *|* Hamilton, ON, L8S 4L8 > 905 525 9140 x24784***|*lindsay.hanf...@gmail.com > <mailto:lindsay.hanf...@gmail.com> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harva

Re: [Freesurfer] converting .nii to .mgz

ing 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.n

Re: [Freesurfer] converting .nii to .mgz

s is a user error- sorry about that. > > Thanks, > m > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, January 20, 2015

Re: [Freesurfer] converting .nii to .mgz

mgh.harvard.edu/fswiki/BugReporting >>> >>> >>> Thanks so much, >>> Mia >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mai

Re: [Freesurfer] converting .nii to .mgz

anks again for > all your help, > m > > ________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, January 20, 2015 2:57 PM &g

Re: [Freesurfer] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model

er University *|* 1280 Main Street West, PC329 Psychology > Building *|* Hamilton, ON, L8S 4L8 > 905 525 9140 x24784***|*lindsay.hanf...@gmail.com > <mailto:lindsay.hanf...@gmail.com> > > > ___ > Freesurfer mailing list > Freesur

Re: [Freesurfer] mri_cnr and bash

; 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.

Re: [Freesurfer] Parcellated regions as masks?

ing 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 FileD

Re: [Freesurfer] Correspondence between label vertex number and time course

> 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.m

Re: [Freesurfer] Parcellated regions as masks?

ct syntax that should be > used)? Also, what should i do if I want individual masks for each ROI? > Cheers, > Sabin Khadka > > ------------ > *From:* Douglas N Greve > *To:* freesurfer@nmr.mgh.harvard.edu > *Sent

Re: [Freesurfer] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model

ology > Building *|* Hamilton, ON, L8S 4L8 > 905 525 9140 x24784***|*lindsay.hanf...@gmail.com > <mailto:lindsay.hanf...@gmail.com> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mg

Re: [Freesurfer] mri_cnr and bash

26 >>>>> lh CNR = 1.633 >>>>> white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4 >>>>> gray/white CNR = 2.205, gray/csf CNR = 0.937 >>>>> rh CNR = 1.571 >>>>> total CNR = 1.602 >>> &q

Re: [Freesurfer] QDEC group comparisons

.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.harvar

Re: [Freesurfer] using -cw256 as default is good?

by default to all my scans even for those with > FOV=256 that do not need such flag? > > Thanks > > Best regards > > Dani > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mai

Re: [Freesurfer] average values per cluster

actly the same cluster, but in an independent group not > used in the analysis, for post-hoc comparisons in SPSS? > > Thanks, > > Maaike > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.

Re: [Freesurfer] Some questions about fsaverage

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. > > > > > &g

Re: [Freesurfer] cortical thickness analysis

gt; > > > ___ > 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

Re: [Freesurfer] vertex-wise covariate for gyrification index

t;> >> 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 >

Re: [Freesurfer] FREESURFER] ERROR: matrix is ill-conditioned or badly scaled, condno = 164365

rix above > > > > thanks, > > H.A. LEE > > > > > ___________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-

Re: [Freesurfer] retinotopy in subject volumetric space

ct > --hemi rh --fillribbon --merge vol.angle.mgz --o vol.angle.mgz > > doug > > > On 12/18/14 1:24 PM, Benjamin Zimmerman wrote: >> I mean the individual's anatomical volumetric space. >> >> On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve >

Re: [Freesurfer] MNI to RAS?

> Thanks! > > Cat > > > > ___ > 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 Ph

Re: [Freesurfer] average values per cluster

nteraction is /not /significant > > > (corrected for the same covariates as in the FSGD file). > > > > > > Could you tell me what is going wrong here? I do not trust my > results now. > > > > > > Furthermore, is it possible (and if so, how?) to extract the

Re: [Freesurfer] extracting pvalues

___ >> 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.m

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

t;>>>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe >>>>>>>>>>> to the NeuRA Magazine >>>>>>>>>>> <http://www.neura.edu.au/help-research/subscribe> >>>>>

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

ps://twitter.com/neuraustralia>Follow NeuRA on facebook > <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to > the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> > > On 5/02/2015 3:16 am, Douglas N Greve wrote: >> I'm not sure that I understand

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

> Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 > > neura.edu.au <http://neura.edu.au> > > Follow @neuraustralia on twitter > <https://twitter.com/neuraustralia>Follow NeuRA on

Re: [Freesurfer] V1 masking

_ > 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: 617-72

Re: [Freesurfer] Creation of the aseg.stats table fails when only running -autorecon1 or -autorecon2

reesurfer@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.

Re: [Freesurfer] Freesurfer could not accurately recognize the voxel size

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 informat

Re: [Freesurfer] average values per cluster

I) values from > a certain cluster. > > > > > > > > > > As I understood, the abs.y.ocn.dat file gives > the average values > > > for a > > > > >

Re: [Freesurfer] bbregister error [Was: TRACULA mask error]

and the part was not >>>>>>>> included in >>>>>>>> the brain mask), or that there was misregistration between the >>>>>>>> T1 and >>>>>>>> diffusion. You can troubleshoot this by looking at the >>

Re: [Freesurfer] DTI question

se 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. > > >

Re: [Freesurfer] V1 masking

that includes the probabilities of a voxel being on V1. > > is this possible? > > many thanks! > david > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.h

Re: [Freesurfer] freeview registration

pLine 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

Re: [Freesurfer] funcroi-table-sess error, "variable must begin with a letter"

> > > ___ > 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 Num

Re: [Freesurfer] cluster colors

> > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurf

Re: [Freesurfer] Register.dof

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. > > > ___

Re: [Freesurfer] Surface-based Interhemispheric Registration generate average surface from average subject

hile, the generation of the surfaces from the data > which have already been computed would be very helpfull. Is it possible to do > that? > > Yours pfannmoe > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 B

Re: [Freesurfer] mris_preproc skips subjects

ing to make. > I'm running ver. 5.3.0 > > What is wrong? > > All the best, > Anders > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > &

Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638

> 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 p

Re: [Freesurfer] Creating subject-wise functional ROIs on the cortical surface

> --- > Eric A. Reavis, Ph.D. > Postdoctoral Scholar > Semel Institute for Neuroscience and Human Behavior > UCLA > (310) 478-3711 ext. 43382 > > > ___ > Frees

Re: [Freesurfer] Using -qcache command multiple times

ead and run the command for all subjects? > > Thank you, > Anne Park > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D.

Re: [Freesurfer] Desikan-Kilany atlas

om 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,

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

g sig.mgh with the one from the lme analysis > - running `mri_glmfit-sim --cache` > > How would I extend this to my case where I don't have pairwise images, but 1 > image for some participants, for others up to 4? > > Thanks a lot, > > Janosch > > > > -- Dou

Re: [Freesurfer] What exactly was wrong with DOSS in QDEC

___ > 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.har

Re: [Freesurfer] Lta_convert

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

Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer

are no data points visible. >> >> Any help would be great as several other functions that I have tried seem to >> be obsolete, >> >> Thanks! >> Sarah >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mg

Re: [Freesurfer] mri_surfcluster questions

abel [--fdr .05 | --thmin 3] --thsign [pos | neg | > abs] > > Thanks, > > Janosch > > > ___ > 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.

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

he 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 pat

Re: [Freesurfer] Regression coefficient qdec

t possible? > > best > Eric > > > ___ > 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.n

Re: [Freesurfer] Bad design matrix

//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 >> >

Re: [Freesurfer] Monte Carlo Simulation

let me know if you have any > additional questions! > > Thanks, > Rick -- 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/f

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

r dir_of_my_simulation -s session_ID > > Regards, > > Antonin > > -------- > *From:* Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > *To:* Antonin Skoch [mailto:a...@medicon.cz] > *Sent:* Mon, 02 Mar 2015 21:07:36 +0100 > *Subject:* Re: [Freesurfer] multiple compa

Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer

esurfer mailing list > 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

Re: [Freesurfer] Bad design matrix

in this case patients) and are zero or constant in > the other. > > Best, > Anders > > 2015-03-02 21:21 GMT+01:00 Douglas N Greve : >> It looks like the 4th column is always -0.9 and the 6th col is always >> -9.138 which makes them redundant with column 2 and causes the e

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

015 um 11:30 schrieb Douglas N Greve : > >> You would do the long analysis using a random effects analysis. > OK, so basically do 2-stage modeling > (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right? > >> For each subject you can get a slope (this won

Re: [Freesurfer] Mapping Own DK Regional Stats onto Surface

and destroy all copies of the original. > > > ___ > 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.

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

t > - use --osgm flag for one-sample group mean Yes > > 5.) replace sig.mgz file with the one from LME analysis and run mri_glmfit-sim Yes > > Is that correct? (especially, is using --do-avg what you meant by taking the > offset) > > Thanks, > > Janosch > > &

Re: [Freesurfer] from vol timecourse to surf timecourse

get the resulting fstcmc.ni.gz on to the > fsaverage surface using spherical alignment? > > Jan > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve

Re: [Freesurfer] tksurfer overlay threshold

attached, on the left)? > > Thank you! > > Gabriella > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR C

Re: [Freesurfer] Mapping Own DK Regional Stats onto Surface

ay file? > > Thank you for your assistance, > Tony > > Tony Jin > Data Technician > Dept. of Psychiatry > Stony Brook Medicine > > From: Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>> > Reply-To: "freesurfer@nmr.mgh.harvard.edu > <mailto

Re: [Freesurfer] order of fMRI prepro

r name wrongly in my previous email. > Thank you for quick response. > I am very pleased that one can run FsFast so flexibel. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] fsFast by Octave - minor problems

Mental Health > Czech Republic > > > ___ > 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

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

mris_preproc might work. You could also use mri_concat (mris_preproc is a front end for mri_concat) On 03/03/2015 06:19 PM, Janosch Linkersdörfer wrote: > > Am 03.03.2015 um 14:42 schrieb Douglas N Greve : > >> Some of this Martin will have to comment on, but my comments below

[Freesurfer] Fwd: OHBM Glass Brain Award Reminder: Nomination Deadline March 13th

fyi Forwarded Message Subject:OHBM Glass Brain Award Reminder: Nomination Deadline March 13th Date: Wed, 04 Mar 2015 11:20:59 -0600 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

whm --s fsaverage --hemi lh --smooth-only --i > lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask > brain.fsaverage.lh.mgh// > / > > Many thanks in advance !! > > Best regards, > > - > Matthieu Vanhoutte, MSc > Rese

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

--o lh.fwhm3.fsaverage.cbf.mgh > --mask brain.fsaverage.lh.mgh// > / > > Many thanks in advance !! > > Best regards, > > - > Matthieu Vanhoutte, MSc > Research Engineer - Department of Neuroradiology > Regi

Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

> >> >> ___ >> Freesurfer mailing list >> 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 t

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

mmand lines ? > > - > Matthieu Vanhoutte, MSc > Research Engineer - Department of Neuroradiology > Regional University Hospital, Lille, France > > 2015-03-05 16:45 GMT+01:00 Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>>: > > > >

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

-cortex --tval > lh.fwhm3.fsaverage.cbf.mgh --tfmt curv > > > / > But you told me : > /BTW, why are you changing format from w to curv? > Why use curv at all? I'd use mgz or nifti. > > / > At this point I don't know what this means ? > >

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