Re: [Freesurfer] GLM_ functional connectivity analysis

I did not doug On 04/29/2015 01:19 PM, Alshikho, Mohamad J. wrote: > Hi Doug, > I sent you the files. I hope you got them > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas

Re: [Freesurfer] Viewing gfeat results on inflated brain

. >> >> Thanks, >> Ghazal Kiani >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > __

Re: [Freesurfer] mri_mcsim with different threshold

; for > > > a subset of p value, and looking in the help, it seems that there is > > > no way of overcome this behavior. > > > Is there another way to obtain the correct threshold value for p =.1 ? > > > > > > Thanks in adance > > >

Re: [Freesurfer] Tksurfer_fminmax flag

to calculate those values depending on the CWP for every > structure in "cache.th30.pos.sig.cluster.nii.gz" > > > Thanks, > Mohamad > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.m

Re: [Freesurfer] mri_glm --wls flag

eesurfer@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/mailm

Re: [Freesurfer] mri_glm --wls flag

Fit completed in 0.0136167 minutes > Computing spatial AR1 on surface > WARNING: ar1 = 0 <= 0. Setting fwhm to 0. > Residual: ar1mn=0.00, ar1std=0.00, gstd=0.00, fwhm=0.00 > Writing results >Contrast1group.diff > maxvox sig=1e+10 F=0 at index 21

Re: [Freesurfer] FreeSurfer Correction

> > Thanks, > Ghazal > > > ___ > 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 Pho

Re: [Freesurfer] qcache command after already running recon-all without it

vard.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

Re: [Freesurfer] 2 factor design. error: matrix is ill-conditioned or badly scaled

0.000 0.000 0.000 0.000 31.200 0.000 >>> 0.000 0.000 0.000; >>> ---- >>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >>> >>> Possible problem with experimental des

Re: [Freesurfer] FW: Re: ERROR: matrix is ill-conditioned or badly scaled

lands > > Tel: +31 20 4448527 Room: PK -1 Z 039 > > > > ___________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Cente

Re: [Freesurfer] make_average_subject

o create an average? >> >> Thanks so much >> >> Jane. >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>

Re: [Freesurfer] FSFAST_Volume based analysis

-mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2.01 -per-run -force > > > But when I ran the command mri_glmfit. It called me that the flag --surface > hemi is missing > > > I highly appreciate any advice > Thank you > > Mohamad > >

Re: [Freesurfer] Exporting the Hippocampus

. >> >> Thank you, >> Chester > > ___________ > 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.harv

Re: [Freesurfer] Fwd: F-test with mkcontrast

se each a and c are assumed to be from different vectors, not from one > vector. I'd appreciate if anyone could help me.| > | > | > |Best wishes,| > |James| > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.har

Re: [Freesurfer] DTI tensor estimation

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/Bug

Re: [Freesurfer] Exporting the Hippocampus

this, please let me know). > > Thanks, > Chester > > >> On May 8, 2015, at 1:28 PM, Douglas N Greve >> wrote: >> >> do you mean the hippocampus in aseg.mgz or the hippocampal subfields? >> >> On 05/08/2015 01:26 PM, Chester Dolph wrote: >>>

Re: [Freesurfer] Exporting the Hippocampus

the same coordinate space so > comparisons may be made between MRI scans. > > By “extract”, I mean isolate the ROI and ignore all other volumes. > >> On May 8, 2015, at 2:54 PM, Douglas N Greve >> wrote: >> >> when you say "extract" what do you mean ex

Re: [Freesurfer] DTI tensor estimation

ares? > > - Anders > > > Från: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] för Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Skickat: den 8 maj 2015 19:40 > Till: freesurfer@nmr.mgh.harvard.edu > Ämne: Re: [Freesurf

Re: [Freesurfer] Interaction contrast setup

_ > 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

[Freesurfer] Fwd: OHBM 2015 Council Election Deadline

Forwarded Message Subject:OHBM 2015 Council Election Deadline Date: Mon, 11 May 2015 10:52:06 -0500 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu The election process to select your organizational le

Re: [Freesurfer] Fcseed-sess

t; > > Regarding the command fcseed-sess how can I force it to find voxels in the > final mask? > > Thanks, > Mohamad > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve,

Re: [Freesurfer] Demeaning both covariates of interest as well as nuisance for only one group

variable (as according to Mumford: "mean > centering a covariate will never change the inference for that > covariate"). Any input would be great. Thank you. > > Paul > > > ___ > Freesurfer mailing list > Freesurfer@nmr.m

Re: [Freesurfer] Fcseed-sess

Found 0 values in range > Counting number of voxels > Found 16777216 voxels in final mask > mri_binarize done > > > Thank you for any advice? > > Mohamad > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Grev

Re: [Freesurfer] xhemi final iteration

Derek Dean > Department of Psychology and Neuroscience > University of Colorado Boulder > > > > > > > ___ > 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 g

Re: [Freesurfer] references for qdec/mcsim methods

othing was of 14 mm FWHM. Which study > can I reference for glmfit and MC simulation method in freesurfer ? > > Thank in advance > > Alain > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mai

Re: [Freesurfer] dt_recon

data is usual. > I would appreciate help in regard of how to deal with this data and > input it into dt_recon. > Regards, > Pedro Rosa. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.

Re: [Freesurfer] a mkanalysis-sess question

lieve 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

Re: [Freesurfer] interpreting glmfit-sim results

er 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:

Re: [Freesurfer] FSFAST_Paradigm file

hanks > > Mohamad__ > > > > ___ > 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

Re: [Freesurfer] aparc labels to grey white ratio

_ > 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 File

Re: [Freesurfer] question regarding the contrast in mri_glmfit

. > > Sincerely, > > Alena > > > > > _______ > 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

Re: [Freesurfer] Interaction contrast setup

tle STX > Class Male > Class Female > VariablesAge_demeanedEdu_demeanedFactor1Factor2 > InputF01_1Female-5.08891.85560.90.93 > InputF02_1Male1.9111-0.14440.850.85 > > On Fri, May 8, 2015 at 3:51 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > what are

Re: [Freesurfer] mni152reg fails due to write permissions

urfer@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

Re: [Freesurfer] Whitening in FSFAST

ion? > Thanks, > Caspar > > > > > > ___ > 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: 617-726-74

Re: [Freesurfer] problem with mris_label2annot

. Any ideas what I'm doing wrong? > > Thanks, > > Aaron > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph

Re: [Freesurfer] isxconcat-sess

in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Gr

Re: [Freesurfer] xhemi final iteration

las.i2.sphere.reg --fsgd laterality.fsgd --xhemi --lh > > > ___ > 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] xhemi final iteration

l.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/faci

Re: [Freesurfer] xhemi final iteration

attached a text document of the output. > > > ___ > 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.harv

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

ist > 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.nm

Re: [Freesurfer] fcseed-sess error

atanner > UseRobust 0 > Loading > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii > Loading > /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/fmcpr.nii > Voxel Volume is 27 mm^3 > Generating list of segm

Re: [Freesurfer] fcseed-sess error

an/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/avgwf.mgh > $Id: mri_segstats.c,v 1.113 2015/05/05 22:32:40 nicks Exp $ >>> cwd >>> cmdline mri_segstats --i >>> /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/fmcpr.nii > --se

Re: [Freesurfer] fcseed-sess error

514/seg.nii >>> frame 0 >>>>> nErode3d 0 >>>>> nErode2d 0 >>>>> output >>>>> /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii >>> Binarizing based on matching values

Re: [Freesurfer] Custom LookUp Table

eft-Hippocampus220 216 20 0 > # 18 Left-Amygdala > … > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > --

Re: [Freesurfer] fs-fast primarily voxel based?

___ > 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 Bu

Re: [Freesurfer] average subject

be the problem? > > Thank you in advance. > > Best regards, > Sofia > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu

Re: [Freesurfer] Diffrence Between stat files and mris

mygdala volume! > Kind regards > > > > ___ > 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

Re: [Freesurfer] mris_label2annot: surf/rh.orig No such file or directory

> ___ > 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 in

Re: [Freesurfer] switch to freesurfer

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

Re: [Freesurfer] switch to freesurfer

doug On 05/26/2015 01:06 PM, Melissa Levesque, Ms. wrote: > It's an analysis to assess correlations in cortical thickness or surface area > across the cortex or with a predictor variable. > > http://www.bic.mni.mcgill.ca/~jason/reprints/Lerch2006MACACC.pdf > > -- Dou

Re: [Freesurfer] WM ROIs: Using wmparc.mgz from cvs_avg35_inMNI152 atlas

> 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

Re: [Freesurfer] error mni152 reg

2.2mm.dat > > --dof 12 > mkdir: cannot create directory > `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253': > Permission denied > > > > > > > > ___________ > Freesurfer mailing lis

Re: [Freesurfer] Stats file question

__ > 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] FW: correcting for brain size

on above. You can also run it as a DOSS (different offset, same slope) doug > > I’d really appreciate any help on this. > > Thank you! > > Gabriella > > > > ___________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.

Re: [Freesurfer] Fwd: recon-all issue

gt; 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

Re: [Freesurfer] Custom LookUp Table

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

Re: [Freesurfer] WM ROIs: Using wmparc.mgz from cvs_avg35_inMNI152 atlas

>> >> Estephan J. Moana-Filho, DDS, MS, PhD >> Clinical Assistant Professor >> TMD and Orofacial Pain Division >> U of MN School of Dentistry > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fa

Re: [Freesurfer] --sim: Command not found

me error: --sim: Command not found. > > Does anyone know why I get this error? > > Thanks! > Mihaela > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

Re: [Freesurfer] FW: correcting for brain size

rors, anyway). > > Thank you! > Gabriella > > 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: Wednesday, May 27, 2015 3:23 PM &g

Re: [Freesurfer] Apply ROI Label from first time point to longitudinal template

ered to base (template) subjects(from longitudinal pipeline). > Would you please let me how can I convert the label from 1st time > point space to longitudinal template space? > > Best regards, > Amirhossein Manzouri > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harva

Re: [Freesurfer] FW: correcting for brain size

, Gabriella wrote: > Sure thing, see attached. > > 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: Wednesday, May 27, 2015 4:19 P

Re: [Freesurfer] FW: correcting for brain size

reesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, May 27, 2015 4:35 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FW: correcting for brain size > >

Re: [Freesurfer] --sim: Command not found

rence like here (first contrast): > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V > > Best, > Mihaela > > > On Wed, May 27, 2015 at 4:18 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Are you sure there is not any white space after the backslash (\

Re: [Freesurfer] FW: correcting for brain size

esurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Wednesday, May 27, 2015 4:43 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FW: correcting for brain size > > Hmm, still can't replicate the error. Can you post this file to our filed

Re: [Freesurfer] FW: correcting for brain size

l Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Wednesday, May 27, 2015 5:40 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FW: correcting for brain size > > Oh, sorr

Re: [Freesurfer] Longitudinal fMRI analysis

: +1-617-724-5652 > Email: > mreu...@nmr.mgh.harvard.edu > reu...@mit.edu > Web :http://reuter.mit.edu > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/list

Re: [Freesurfer] FW: correcting for brain size

ol-to-eTIV > MaskVol-to-eTIV > lhSurfaceHoles > rhSurfaceHoles > SurfaceHoles > eTIV > > Is there a way to create it? > > Thanks! > ____ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harv

Re: [Freesurfer] Fwd: recon-all issue

his. doug On 05/28/2015 10:46 AM, anvi vora wrote: > It is attached again. > > I hope it was because kicked off the server, > > Thanks a lot > Anvi > > On Wed, May 27, 2015 at 3:24 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > >

Re: [Freesurfer] FW: correcting for brain size

mething? > > Thanks so much! > > > > 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: Thursday, May 28, 2015 1:37 PM >

Re: [Freesurfer] selxavg3-sess CPU limits

ownregulate the number of CPUs that the script > is using? > Thanks, Caspar > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Gr

Re: [Freesurfer] selxavg3-sess CPU limits

gt; > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f

Re: [Freesurfer] glmfit error

0.000 5.982 0.000 -0.091 0.000 0.880 0.000 > 0.925 0.000 0.814; > 0.000 1.000 0.000 -4.018 0.000 -4.091 0.000 0.750 0.000 > 0.800 0.000 0.600; > 0.000 1.000 0.000 5.982 0.000 -0.091 0.000 0.943 0.000 > 0.850 0.000 0.80

Re: [Freesurfer] GLM analysis on CBF maps

ft /contrasts/: >>> //control-left.intercept.mtx /and///control-left.slope.mtx. /The >>> same for/Control > Right./ One is coding for intercept and the other >>> for slope, but concretely what significative results in both >>> contrasts mean ? >>> >>> Thank you in adva

Re: [Freesurfer] Timecourses In freesurfer

eesurfer@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 FileDro

Re: [Freesurfer] R: mni305 volume-based analysis

.config > > fcseed-sess -s sessionid -cfg wm.config > > fcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config > > fcseed-sess -s sessionid -cfg vcsf.config > > 7. selxavg3-sess -s Sessid -a fc.lthalseed.surf.lh > > selxavg3-sess -s Sessid -a fc.rthalsee

[Freesurfer] acknowledging FreeSurfer on your OHBM Poster

: here are links on how to cite FS in papers, etc http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&do=view&target=freesurfer_methods.doc http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.har

Re: [Freesurfer] R: Re: R: mni305 volume-based analysis

gid 49 -fcname R_Thalamus.dat -fsd rest -mean -cfg > > > > mean.R_Thalamus.config > > > > 5. fcseed-sess -s Sessid -cfg mean.R_Thalamus.config > > > > fcseed-sess -s Sessid -cfg mean.L_Thalamus.config > > > > 6. Create nuisance variables: > > > > fcs

Re: [Freesurfer] [FreeSurfer] Multiple overlays on surface

(0) to be transparent or anything that could solve the mater ? > > Best regards, > > Matthieu > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, P

Re: [Freesurfer] [FreeSurfer] Multiple overlays on surface

what is the terminal output for mris_seg2annot? On 06/05/2015 06:12 PM, Matthieu Vanhoutte wrote: > > I tried it but gave me a black surface. > > Le 6 juin 2015 00:06, "Douglas N Greve" <mailto:gr...@nmr.mgh.harvard.edu>> a écrit : > > Try it with 0 0 0

Re: [Freesurfer] error mri_glmfit-sim

> Thanks, > > > > Stefano > > > > ___ > 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] bad magic number

> >> >> >> I am looking for a lot of men who have an infinite capacity to not >> know what can't be done. >> >> - Henry Ford >> >> >> >> The important thing

Re: [Freesurfer] Align functional to anatomical volume

you think? > > Thank. Best regards. > > > ___ > 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] selx3avg-sess and monkey data

thout aseg.mgz? > > Thanks! > > Jack > > > > ___________ > 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] preproc-sess creates files

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.n

Re: [Freesurfer] sagittal slices

The important thing is not to stop questioning. Curiosity has its own > reason for existing. > > - Albert Einstein > > > > _______ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MG

Re: [Freesurfer] Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

T analysis is > effectively the my ROI_MASK? > > I hope in your help. > > Thanks in advanced. > > > Stefano > > > ___________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Gr

Re: [Freesurfer] help on mris_preproc

incost > rh.sum_all_norm_IRF_HA.mgh sum_all_norm_IRF_HS.nii > > fsaverage lh.sum_all_norm_IRF_MS.mgh register.dat.param > rh.sum_all_norm_IRF_HS.mgh sum_all_norm_IRF_MA.nii > > lh.EC_averagemprage_nudge_RAI.nii.gz > register.dat.sum rh.sum

Re: [Freesurfer] Timecourses In freesurfer

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:

Re: [Freesurfer] Retinotopic mapping

gt; retinotopic mapping (with the correspondent informations about angle > and eccentricity)? > > Thank in advance! > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/lis

Re: [Freesurfer] SMS3 pre-processing

mr.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.h

Re: [Freesurfer] Functional group analysis

__ > 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/fs

Re: [Freesurfer] Extracting values from GLM Clusters

same thing? > > Thanks! > > Andrew Schoen > University of Wisconsin - Madison > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas

Re: [Freesurfer] mni152reg

r 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: http

Re: [Freesurfer] SMS3 pre-processing

> > Best, > Anais > > Sent from my iPhone > >> On Jun 29, 2015, at 6:46 PM, Douglas N Greve >> wrote: >> >> I don't have a way to do SMS stc in 5.3 (it is there for 6.0). You might >> not need it for 1.15s TR. How long are your stimuli? >&g

Re: [Freesurfer] mri_label2label problem revisited

t; > Inline image 2 > > > > > > > > > ___________ > 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] unique label from volume / surface ROIs

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/BugRep

Re: [Freesurfer] Reasons for problems with resampling issues

nt (or have received this e-mail in error) please notify > > the sender immediately and destroy this e-mail. Any > > unauthorised copying, disclosure or distribution of the > > material in this e-mail is strictly forbidden. > > ----------

Re: [Freesurfer] unique label from volume / surface ROIs

1/$2/roi/mask_vol.nii --temp > $1/$2/mri/orig.mgz --subject $2 > > Cheers, > Martin > > > 2015-07-01 23:38 GMT+02:00 Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>>: > > How did you create the ROIs? > > On 07/01/2015 12:25 PM, Martin Hebart wrote:

Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion

urce Subject Surface > 1 0.5 0.5 0.5 > using old > Done mapping volume to surface > Number of source voxels hit = 5 > Writing to PM_04001/bold/lh.sig.mgh > Dim: 126553 1 1 > > > > Thanks, > > Christopher > > >

Re: [Freesurfer] [FreeSurfer] aparc+aseg.mgz unkown voxels

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

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