Re: [Freesurfer] Fwd: Error with experimental design using FSGD

. Thank You for your patience and assistance Joshua ___ 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] Permutation doubts

the permutations with niusance variables? Many thanks in advance, Gabriel ___ 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] stats question

/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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer

Re: [Freesurfer] Permutation doubts

therein. cheers, -MH -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu

Re: [Freesurfer] MNI template

Sciences Via Delle Regole 101, 38123 Mattarello Trento, Italy tel. +39 0461 283083 ___ 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] Contrast file for cortical thickness 2 group 1 covariate analysis

we're looking for. Any advice on what sort of contrast file we should use, or whether we need to run a different analysis than glmfit, would be greatly appreciated! Thanks! Best, Alex -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726

Re: [Freesurfer] Permutation doubts

/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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer

Re: [Freesurfer] Fwd: Error with experimental design using FSGD

if you require any morer files such as the .mgh files. Thank you for your time in this matter. Joshua On Thu, Apr 4, 2013 at 11:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Joshua, you should start by not coding gender and handedness

Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 109, Issue 21

___ 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

Re: [Freesurfer] mri_aparc2aseg issue

/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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu

Re: [Freesurfer] tksurfer partial overlays?

@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: www.nmr.mgh.harvard.edu/facility/filedrop

Re: [Freesurfer] FS-FAST motion correction / register

___ 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

Re: [Freesurfer] Comparing HRF undershoots between conditions

Imaging Center, MGH Harvard Medical School -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp

Re: [Freesurfer] Comparing HRF undershoots between conditions

for the delay you want to see. doug On 04/10/2013 04:15 PM, SHAHIN NASR wrote: That's the problem Doug. I have already generated the FIR model but how can I show the sig MAP for one particulat time point. What are the other ways? On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve gr

Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

? Regards That's the problem Doug. I have already generated the FIR model but how can I show the sig MAP for one particulat time point. What are the other ways? On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Shahin, there are several ways that you could do

Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

the response maps relative to the baseline. On Apr 10, 2013 6:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: yes, that is what you want. The only other way that comes to mind is to model each event type as two event types one delayed

Re: [Freesurfer] mri_aparc2aseg issue

___ 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

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

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

Re: [Freesurfer] DTI: problems with (high) FA values

-- 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: www.nmr.mgh.harvard.edu/facility

Re: [Freesurfer] final skull-stripped file?

...@nmr.mgh.harvard.edu mailto:ma...@nmr.mgh.harvard.edu ___ 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

Re: [Freesurfer] mri_glmfit .nii.gz FSF_OUTPUT_FORMAT

___ 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

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

...@nmr.mgh.harvard.edu *À :* Michael Harms mha...@conte.wustl.edu *Cc :* Lucille Deroche lucilledero...@yahoo.fr; freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu; Douglas N Greve gr...@nmr.mgh.harvard.edu *Envoyé le :* Jeudi 11 avril 2013 16h02 *Objet :* Re: [Freesurfer] Autoreg-sess

Re: [Freesurfer] mkbrainmask error with libmeshclass.so

1 binvalnot 0 ___ 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

Re: [Freesurfer] recon-all -autorecon2 bug?

___ 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

Re: [Freesurfer] QDEC questions

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

Re: [Freesurfer] register.dat

.. ___ 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

Re: [Freesurfer] gender differences in qdec

does it mean? There can not be a negative difference...?? Thank you very much! Leni ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR

Re: [Freesurfer] T2 pial

://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

Re: [Freesurfer] gender differences in qdec

22.04.2013 um 15:56 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Hi Lena, it is not a difference, it is a correlation between thickness and BIS. The sentence produced by QDEC would be clearer if you gave the groups actual names instead of 0 and 1. doug

Re: [Freesurfer] merging dti data

congrats! On 04/23/2013 02:13 PM, Jon Wieser wrote: Hi Doug we got good results with the dit of the merged brik's Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday

Re: [Freesurfer] asegstats2table error depending on subject sorting

the subjects list is attached, sorted the way it produces the error greetings, Andreas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR

Re: [Freesurfer] smooth overlay

___ 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

Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: yes, that is what you want. The only other way that comes to mind is to model each event type as two event types one delayed relative to the other. Then model the responseto each as a gamma

Re: [Freesurfer] convert phillips PAr/Rec files

I use? JoPhone: 414-229-7145 -- 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

Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

wrote: I know but how can we generate negative coefficient? To clarify, we use alpha=2, delta=2.25 tau=1.25 to generate default HRF. Using negative values for alpha, delta or tau, does not invert the shape of the curve (HRF). On Wed, Apr 24, 2013 at 3:12 PM, Douglas N Greve gr

Re: [Freesurfer] Fwd: Conversion

mailto:gariko...@gmail.com Date: Sat, Apr 20, 2013 at 2:31 AM Subject: Conversion To: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Hi Doug, sorry to bother you again with a direct message, one of your colleagues has been helping out but I don't think he got

Re: [Freesurfer] convert labels to volumetric masks

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] mri_glmfit --no-sim error: cannot find any csd files

/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

Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd 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

Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files

Douglas N Greve Thu, 25 Apr 2013 14:08:32 -0700 what was your orignal mri_glmfit-sim command line? On 04/25/2013 05:17 PM, Jeni Chen wrote: Hi Doug, Sorry; didn't realize it wasn't included. So to state the original problem, I tried running mri_glmfit-sim with the following options

Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files

\ --cwpvalthresh .999 \ --no-sim 1GroupAvg-Cor-thickness-Mod-VAS And it did not work either. Thanks. jeni Douglas N Greve Thu, 25 Apr 2013 14:08:32 -0700 what was your orignal mri_glmfit-sim command line? On 04/25/2013 05:17 PM, Jeni Chen wrote: Hi Doug, Sorry; didn't realize it wasn't

Re: [Freesurfer] question on mri_segstats

/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

Re: [Freesurfer] ROI analyses

://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

Re: [Freesurfer] Freesurfer Digest, Vol 109, Issue 21

that the green area in not big enough, is this fixable ? Thanks ! Rotem ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve

Re: [Freesurfer] convert labels to volumetric masks

this goal, and which commands should I use. Thanks a lot. Best wishes, Meng Date: Mon, 29 Apr 2013 17:30:14 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] convert labels to volumetric masks To: freesurfer@nmr.mgh.harvard.edu Message-ID: 517ee666.8050

Re: [Freesurfer] Exiting with errors but not sure why

why. I've attached the error.log, but le tme know if I should attach another file. Thanks so much, Mia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve

Re: [Freesurfer] mri_glmfit-sim - error of fwhm

) but not 0. I have to add an argument to specify fwhm used ? Thank you for your help ! Best regards. Sophie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N

Re: [Freesurfer] FLASH params for mri_em_register

. -- 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

Re: [Freesurfer] Exiting with errors but not sure why

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 02, 2013 11:45 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Exiting with errors

Re: [Freesurfer] FLASH params for mri_em_register

are switched (in talaiarch.lta, the .gca is the dst, whereas in new output file, it's the src). Also, the RB...gca is 256 256 256 in the original lta, whereas in the new one (where it's src) it's 128 128 128, which agrees with mri_info output. cheers, Fred On 2 May 2013, at 17:13, Douglas N Greve

Re: [Freesurfer] FLASH params for mri_em_register

talaiarch.lta with the correct geometry so that mri_ca_normalize/register will read it right? On 2 May 2013, at 18:04, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Fred, so do you still have an outstanding question? doug On 05/02/2013 12:55 PM, Fred Dick wrote: Hi Doug totally

Re: [Freesurfer] epi correction of fmri data

___ 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

Re: [Freesurfer] Using mri_cor2label

___ 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

Re: [Freesurfer] Issues with Cluster generation

is the cluster generation dependent upon? As my glmfit does show significant areas. Please advise ___ 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] determine the peak vertex

! Best wishes, Meng ___ 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

Re: [Freesurfer] epi correction of fmri data

lines. doug On 05/03/2013 12:16 PM, Corinna Bauer wrote: Yes, I am using FSFAST. On Fri, May 3, 2013 at 12:08 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Corinna, are you using FSFAST? If not, are you still going to the surface? doug

Re: [Freesurfer] epi correction of fmri data

? On Fri, May 3, 2013 at 12:30 PM, Corinna Bauer corinna...@gmail.com mailto:corinna...@gmail.com wrote: thanks Doug, I will give that a try. On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Create the B0

Re: [Freesurfer] epi correction of fmri data

What is going wrong when you run FSL 5? On 05/03/2013 01:38 PM, Corinna Bauer wrote: oh great. Is there a way to get this to work with FSL 5? On Fri, May 3, 2013 at 1:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It needs to be 0 to 4095

Re: [Freesurfer] epi correction of fmri data

, May 3, 2013 at 1:42 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: What is going wrong when you run FSL 5? On 05/03/2013 01:38 PM, Corinna Bauer wrote: oh great. Is there a way to get this to work with FSL 5? On Fri, May 3

Re: [Freesurfer] epi correction of fmri data

) then if ( $FSLVerMaj == 4 ) then if ( 5 == 4 ) then echo FSL Version is $FSLVersion, must be 3.X or 4.X echo FSL Version is 5.0.2, must be 3.X or 4.X FSL Version is 5.0.2, must be 3.X or 4.X exit 1 ; exit 1 On Fri, May 3, 2013 at 2:09 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr

Re: [Freesurfer] epi correction of fmri data

, May 3, 2013 at 2:28 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I can't remember why I excluded version 5. I put another version herethat will accept v5 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl try

Re: [Freesurfer] epi correction of fmri data

images right from the get-go instead of raw fmri runs? On Fri, May 3, 2013 at 4:04 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: yep, it is basically the same error On 05/03/2013 03:57 PM, Corinna Bauer wrote: I would imagine so. I

Re: [Freesurfer] epi correction of fmri data

, 36, 245) On Fri, May 3, 2013 at 4:36 PM, Corinna Bauer corinna...@gmail.com mailto:corinna...@gmail.com wrote: It did run all the way through using the .img files. Should I try that mri_convert on all 4 real/imaginary files? On Fri, May 3, 2013 at 4:30 PM, Douglas N Greve

Re: [Freesurfer] The Asymmetry of surface area or thickness

___ 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

Re: [Freesurfer] Probably activation due to vessels

-fwhm 5 -fsd bold -s sess01 ... . On Fri, 19 Oct 2012 12:49:00 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to run preproc like: preproc-sess -per-session -fwhm 5 -fsd bold -s sess01 In this case, you are just specifiying -per-session and not specifying -mni305

Re: [Freesurfer] Issues with Cluster generation

the image is : tksurfer fsaverage lh inflated -annot lh.thomasR.glmdir/RC.txt/mz-z.negative.sig.ocn.annot fthresh 1 -curv -gray The version of freesufrer i'm using is 1.379.2.17 Thank you helping me out with this. On Sat, May 4, 2013 at 12:12 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu

Re: [Freesurfer] ROI analyses

___ 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

Re: [Freesurfer] segfault during rfx with mri_glmfit

@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

Re: [Freesurfer] Probably activation due to vessels

an error message, but have attached a log file to this mail. A solution of this problem would help me to simplify my workflow and improve the analysis. Thanks in advance. Joerg On Mon, 06 May 2013 10:48:14 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: If you use -per-session

Re: [Freesurfer] Using FSL matrix for Talairach transform

/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

Re: [Freesurfer] Segstats

___ 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

Re: [Freesurfer] Labels and parcellations

___ 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

Re: [Freesurfer] Labels and parcellations

, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 05/08/2013 11:43 AM, Tudor Popescu wrote: Hello all, I have some more burning questions, for which I thank you in advance!! 1) I expected that mri_annotation2label

Re: [Freesurfer] Labels and parcellations

, it is the 4th button from the right on the top row. It will say Draw Filled Labels when you put the mouse over it On 8 May 2013 16:54, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr

Re: [Freesurfer] ICV

...@gmail.com wrote: Thank you! Sent from my iPhone On May 8, 2013, at 8:17 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Alejandra, I don't work with children, so I'll let someone else (Lilla? Rudolph?) answer

Re: [Freesurfer] Qdec error and design problem

-- 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

Re: [Freesurfer] Labels and parcellations

in Fig 1 of the Desikan paper) I don't understand what you mean here. The name of the structure should appear in the control window. It does not appear in the image window like in Fig 1. doug I really appreciate your patience Doug, thanks :) Tudor On 8 May 2013 18:56, Douglas N Greve gr

Re: [Freesurfer] Using FSL matrix for Talairach transform

registration matrix. Thanks for your help! Cheers, Johannes Douglas N Greve Wed, 08 May 2013 12:16:36 -0700 Hi Johannes, as a quick fix can you try inverting the matrix? doug On 05/08/2013 01:31 PM, Johannes Klein wrote: Hi Doug, Thanks for your reply! I'm getting closer to a solution

Re: [Freesurfer] Why does smoothing make non-zero intensity to zero in many vertices?

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

Re: [Freesurfer] smoothing result with larger size FWHM kernel

from slap EPI) ___ 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] Correction for multiple comparisons question

@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] Restricting ROI Analysis

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

Re: [Freesurfer] optseq2 malloc memory / matrix rank-deficient

@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

Re: [Freesurfer] Different freesurfer version

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] Resting state 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/fswiki

Re: [Freesurfer] Very simple question about Paired Analysis

/ji_scripts/lh.paired-diff.thickness.sm05.mgh *ERROR: you must use '--surface subject hemi' with surface data* -- 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] rs-fMRI data on pial surface

, René ___ 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

Re: [Freesurfer] Still confused by group analysis..

/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

Re: [Freesurfer] Still confused by group analysis..

help me to address this problem. I'm CC'ing FSL list so others may also help. All the best, -Arman On Tue, 2013-05-14 at 12:04 -0400, Douglas N Greve wrote: On 05/14/2013 10:05 AM, Tudor Popescu wrote: I thought that it would have. Are you coding age as a nuisance variable? Also, are you

Re: [Freesurfer] averaging lh and rh thickness maps on fsaverage_sym surface

@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

Re: [Freesurfer] problem with func2roi-sess

}/${identifier}_recon/label/MedOrbitofrontal_LH_${identifier}.label. Thank you! Jeff ___ 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] mri_glmfit error with design matix

; -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D

Re: [Freesurfer] rs-fMRI data on pial surface

this actually results in a projection of the white surface, but I guess this actually doesn't matter since each white vertex is associated to a directly overlying pial vertex? Best regards, René On Tue, May 14, 2013 at 5:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr

Re: [Freesurfer] Still confused by group analysis..

a /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t find a log file from make_average_subject so i don’t know if it gave any errors.. It's extremely helpful to have command lines ... Thanks again Doug! -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number

Re: [Freesurfer] new version

___ 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

Re: [Freesurfer] problem with func2roi-sess

/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

Re: [Freesurfer] The v5.3 release is here

@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

Re: [Freesurfer] FMRI surface transformation for vertex-wise connectivity analysis

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

Re: [Freesurfer] Fsaverage b0

@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] QDEC and Hippocampal subfields

-- 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

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