Re: [Freesurfer] fslaverage/MNI coordinates

2016-07-07 Thread Douglas N Greve
> I guess I can then get the MNI152 coordinates in this way: > > P305 = [MNI305x MNI305y MNI305z 1]'; > P152 = M*P305 > > Am I correct? > > Best wishes, > Baojuan > > > From: freesurfer-boun...@nmr.mgh.harvard.

Re: [Freesurfer] make_average_template error

2016-07-07 Thread Douglas N Greve
Linux 7.1 with 48 core > memory. > > I was wondering if you could possibly provide any advice for > troubleshooting this error. > > Best wishes, > Vasiliki > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mai

Re: [Freesurfer] question about volume of the hippocampus

2016-07-07 Thread Douglas N Greve
he volume of the hippocampus? > I and very looking forward to hearing from you. > > Yours sincerely, > Junji Komatsu > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] PVE correction tool on Freesurfer 6

2016-07-07 Thread Douglas N Greve
ats > > for writing// > //Errno: No such file or directory/ > > > > Thanks a lot in advance, > > Regards, > Subin > > > > ___________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nm

Re: [Freesurfer] continuity in volumes converted from labels

2016-07-07 Thread Douglas N Greve
ce. > > Shads > > > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > ___________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https:

Re: [Freesurfer] mapping a surface from fsaverage_sym to the subject's native surface

2016-07-07 Thread Douglas N Greve
I answered this yesterday On 07/06/2016 01:47 PM, Douglas N Greve wrote: > > It would be something like > mris_apply_reg --src lh.data-from-fsavgsym.mgh --streg > $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg > $SUBJECTS_DIR/yoursubject/surf/lh.fsaverage_sym.sphere.reg --o

Re: [Freesurfer] Design Matrix Creation

2016-07-07 Thread Douglas N Greve
fferences amongst diagnosis and study > > > > site. > > > > > > > > 2) Allowing a difference in age slope amongst the diagnosis levels > > > > > > > > 3) Modeling the age slope as the same for the study site levels > > > > >

Re: [Freesurfer] BrainSeg Volume Clarification

2016-07-07 Thread Douglas N Greve
Engineering | Class of 2017 > BMES at Ohio State | Professional Development Chair '16-'17 > IBRC| Undergraduate Research Assistant > > 440-623-4710 > cook.1...@osu.edu <mailto:cook.1...@osu.edu> > > > > > __

Re: [Freesurfer] FS V6.0 GTM PVC ROI definition

2016-07-07 Thread Douglas N Greve
did not make much of a difference. doug > > > Thanks, > Pradeep > > > > ___ > 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

Re: [Freesurfer] cache.th13.neg.sig.cluster.mgh directionality

2016-07-08 Thread Douglas N Greve
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 Fax: 617-726-7422 Bugs:

Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3() failed\n

2016-07-08 Thread Douglas N Greve
; * fcseed-sess -s subj439rest -cfg vcsf.config > > STEP7 > > mkanalysis-sess-analysis fc.lpccseed.surf.lh -surface fsaverage lh > -fwhm 5 -notask-taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 > -nuisreg wm.dat 5 -mcextreg-polyfit 5 -nskip 4 -fsd rest -TR 2 -per-run > > STE

Re: [Freesurfer] Mri_glmfit-sim hemisphere correction

2016-07-08 Thread Douglas N Greve
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

Re: [Freesurfer] Fwd: Recon-all exited with errors after mri_nu_correct.mni

2016-07-08 Thread Douglas N Greve
ndidate > > Department of Radiology > Center hospitalier universitaire vaudois (CHUV) and Université de > Lausanne (UNIL) > Rue du Bugnon 46, CH-1011 > > > > > > ___ > Freesurfer mailing list > Freesurfer@n

Re: [Freesurfer] qdec error

2016-07-08 Thread Douglas N Greve
> 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] Question about write_surf.m

2016-07-08 Thread Douglas N Greve
t; > Error in write_surf (line 38) > fwrite3(fid, TRIANGLE_FILE_MAGIC_NUMBER); > > > * > thank you in advance for your help! > Dulce* > * > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

2016-07-18 Thread Douglas N Greve
t_math_monly_EnglishParityRT_a_g_TIV.txt > > --surf fsaverage rh --cortex --glmdir > rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir > 2. The FSGD file (if using one) > 3. And the design matrix above > > > I am also attaching the FSGD file. > &g

Re: [Freesurfer] mri_convert WARNING: files are not found to be different and cannot be sorted

2016-07-18 Thread Douglas N Greve
4 >PhEncDir: ROW > ras xform present > xform info: x_r = 1., y_r = -0.0000, z_r = 0., c_r = > -0. > : x_a = -0., y_a = -0.7593, z_a = -0.6508, c_a = > -41.5207 > : x_s = 0., y_s = -0.6508, z_s = 0.7

Re: [Freesurfer] Beta-Zero Correction - No Phase File

2016-07-18 Thread Douglas N Greve
f Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mail

Re: [Freesurfer] PVE correction tool on Freesurfer 6

2016-07-18 Thread Douglas N Greve
ron or gedit. > They are nifti files, though you probably don't want to use a nifit viewer. You can load them into matlab with MRIread('file.nii.gz') > > Thank you again in adavnce for your help. > > > Best, > > Subin > > -

Re: [Freesurfer] BrainSegVolNotVent

2016-07-18 Thread Douglas N Greve
LUT.txt > --subject SUBJECT_ID --brainmask mri/brainmask.mgz --brain-vol-from-seg > > > Thanks very much for your help! > > Best, > Hamdi > > > > > > _______ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/li

Re: [Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

2016-07-18 Thread Douglas N Greve
rror 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 >

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

2016-07-18 Thread Douglas N Greve
m by the standard deviation? > > Best, > > Jennifer Legault > > On Mon, Jul 18, 2016 at 12:43 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > This is almost surely a problem with scaling as your covariates are > huge. Try subtracting the

Re: [Freesurfer] BrainSegVolNotVent

2016-07-18 Thread Douglas N Greve
> 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: Monday, July 18, 2016 1:33 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] BrainSegVolNotVent > &

Re: [Freesurfer] Comparing between a group of subject

2016-07-18 Thread Douglas N Greve
__ > 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/Bu

Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

2016-07-18 Thread Douglas N Greve
l Research Coordinator > Stufflebeam Lab > Athinoula A. Martinos Center > Massachusetts General Hospital > 149 13th Street, Room 1115S > Charlestown, MA 02129 > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.ed

Re: [Freesurfer] mri_glmfit error

2016-07-18 Thread Douglas N Greve
s dods > Saving design matrix to .//Xg.dat > Normalized matrix condition is 1 > Matrix condition is 1 > Found 121215 points in label. > ERROR: mri_reshape: number of elements cannot change > nv1 = 129318, nv1 = 163842 > Pruning voxels by thr: 0.00 > Segmentation fault >

Re: [Freesurfer] Inquiries about thickness and lgi group analysis

2016-07-18 Thread Douglas N Greve
file view in > Freeview) are exactly the same. Would you please guide me with this? > > Best Regards, > Mahtab. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman

Re: [Freesurfer] Question about NULL event with Optseq2

2016-07-18 Thread Douglas N Greve
eq2 in the right way? How could I fix it? > Thanks in advance & Best regards, > Feng Zhou > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --

Re: [Freesurfer] mri_segstats

2016-07-18 Thread Douglas N Greve
lated to a missing flags in my "mri_segstats" command line? > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, July 7, 2016 12:17 PM > To

Re: [Freesurfer] DeMean Flag

2016-07-18 Thread Douglas N Greve
The DeMeanFlag in what tool? On 07/08/2016 05:16 AM, Clara Kühn wrote: > Dear Freesurfer experts, > > is there an explanation somewhere for the DeMeanFlag? I can't find it in the > wiki but I would like to use it to demean my covariates for the GLM and LME. > > Cheers &

Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

2016-07-18 Thread Douglas N Greve
.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, July 18, 2016 5:23 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error > > Can you run the command below and send me dng.log?

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

2016-07-18 Thread Douglas N Greve
Is this still a problem? If so, can you upload the dicom files to our file drop? On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote: > The file has not been anonymized. > > Thanks, > > Ismail > >> On Jul 5, 2016, at 11:20 AM, Douglas N Greve >> wrote: >> >>

Re: [Freesurfer] FSGD error: class Input not defined

2016-07-18 Thread Douglas N Greve
> National Center of Neurology and Psychiatry (NCNP) > /4-1-1 Ogawahigashi-chyo, Kodaira, > Tokyo 187-8551 Japan/ > > TEL: +81-80-6628-5709 > > 国立精神・神経医療研究センター > 脳病態統合イメージングセンター(IBIC) > 臨床脳画像研究部 画像情報解析研究室 > /〒187-8551 東京都小平市小川東町4-1-1/ > > > > > > >

Re: [Freesurfer] mri_segstats

2016-07-18 Thread Douglas N Greve
egistration is perfect) and the images > are fine. > > I can't explain why this is happening so thank you for any suggestion. > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu]

Re: [Freesurfer] mri_segstats

2016-07-18 Thread Douglas N Greve
> functional images one by one ( the registration is perfect) and the images > are fine. > > I can't explain why this is happening so thank you for any suggestion. > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-bou

Re: [Freesurfer] 3 analyses questions

2016-07-19 Thread Douglas N Greve
> > > ___ > 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: 617-72

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

2016-07-19 Thread Douglas N Greve
with -it dicom. So ... don't use -it dicom On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote: > Hi Doug, > > It is still an issue. I uploaded the DICOMs to you. Hope it could be useful. > Thanks. > > Ismail > >> On Jul 18, 2016, at 6:14 PM, Douglas N Greve >> wr

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

2016-07-19 Thread Douglas N Greve
rs/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 > > does not contain a Siemens ASCII header > has this file been anonymized? > ERROR: cannot unpack mosiacs without ASCII header > > Any idea why ? > > Best, > >

Re: [Freesurfer] Subtracting overlays

2016-07-21 Thread Douglas N Greve
ion >> and Technology >> Karolinska University Hospital | Department of Radiology >> >> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

2016-07-21 Thread Douglas N Greve
1.776 2015/12/17 18:09:34 fischl Exp $ > > > > ___________ > 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] registering subject pial to fsaverage

2016-07-21 Thread Douglas N Greve
d.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in erro

Re: [Freesurfer] registering subject pial to fsaverage

2016-07-21 Thread Douglas N Greve
, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits > = 2.28035 > Saving target data > > > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Thu, Jul 21, 2016 at 11:41 AM, Douglas N Greve > mailto:gr..

Re: [Freesurfer] aparc+aseg.mgz for network analysis

2016-07-21 Thread Douglas N Greve
rfer@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 &g

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

2016-07-21 Thread Douglas N Greve
pos*//* > */ > Note: it is the same code i use for the t-tests, which appear to work > fine. > > The content of the file ${C1} is > > 1 -1 0 0 0 0 > 1 0 -1 0 0 0 > > > Thanks in advance! > > Nicola >

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

2016-07-21 Thread Douglas N Greve
pear to >>> work fine. >>> >>> The content of the file ${C1} is >>> >>> 1 -1 0 0 0 0 >>> 1 0 -1 0 0 0 >>> >>> >>> Thanks in advance! >>> >>

Re: [Freesurfer] mri_glmfit --mask ERROR: dimension mismatch 1 between y and mask

2016-07-21 Thread Douglas N Greve
ombine them but the > output is an annotation file not a label. > > As a note, we will want to do FDR correction, not MC. > > Thanks! > Mihaela > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

2016-07-22 Thread Douglas N Greve
and no > warning) when I use t-tests )i.e. just the first or second line of the > F test). > > Thanks a lot for your time, > > Nicola > > > On 07/21/2016 11:53 PM, Douglas N Greve wrote: >> Try using abs instead of pos. abs (absolute) is more appropriate >&g

Re: [Freesurfer] mri_glmfit --mask ERROR: dimension mismatch 1 between y and mask

2016-07-22 Thread Douglas N Greve
.label --glmdir > lh.group_diff_g2v0.glmdir > > Thanks! > Mihaela > > > On Thu, Jul 21, 2016 at 5:55 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > How did you create the mask? It should be a surface overlay in > fsaverage >

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

2016-07-22 Thread Douglas N Greve
usters and no >> warning) when I use t-tests )i.e. just the first or second line of the F >> test). >> >> Thanks a lot for your time, >> >> Nicola >> >> >> On 07/21/2016 11:53 PM, Douglas N Greve wrote: >>> Try using abs instead of p

Re: [Freesurfer] mri_glmfit --mask ERROR: dimension mismatch 1 between y and mask

2016-07-22 Thread Douglas N Greve
_g2v0.glmdir > > So I used my own label instead of ?h.aparc.annot. Does the above > command look right? > > Thanks again! > Mihaela > > On Fri, Jul 22, 2016 at 12:34 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > What was your vi

Re: [Freesurfer] mri_glmfit --mask ERROR: dimension mismatch 1 between y and mask

2016-07-22 Thread Douglas N Greve
then you need to add --surface fsaverage lh to the mri_glmfit command line, otherwise it thinks it is a volume-based analysis On 07/22/2016 01:58 PM, Mihaela Stefan wrote: > It's surface-based analysis. > > On Fri, Jul 22, 2016 at 1:43 PM, Douglas N Greve > mailto:gr...@nm

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

2016-07-22 Thread Douglas N Greve
h 2016. > > As mentioned in my other mail, I have uploaded a full glmdir at > > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv > > thanks for your time, > > Nicola > > On 7/22/2016 6:35 PM, Douglas N Greve wrote: >> what version does it fail on? If a dev version,

Re: [Freesurfer] mri_glmfit problem/2 group 6 covariates

2016-07-22 Thread Douglas N Greve
elation with second score > compared to group 2 > > sixth contrast matrix > > 0 0 0 0 0 0 0 0 -0.5 0.5 0 0 0 0 > > group2 showing showing increasing correlation with second score > compared to group 1 > > seventh contrast matrix > > 0 0 0 0 0 0 0 0 0 0 0.5

Re: [Freesurfer] mri_glmfit problem/2 group 6 covariates

2016-07-26 Thread Douglas N Greve
to group 1 > > > > > On Mon, Jul 25, 2016 at 11:19 AM, Douglas Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Can you send your new fsgd file and new design matrix? > > > On 7/24/16 6:06 PM, miracle ozzoude wrote: >> Hello Doug o

Re: [Freesurfer] question about reslicing

2016-07-26 Thread Douglas N Greve
; 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 > se

Re: [Freesurfer] normalizing in fsgd

2016-07-26 Thread Douglas N Greve
ended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If th

Re: [Freesurfer] Multiple Comparison Question for surface-based analyses

2016-08-02 Thread Douglas N Greve
I have been doing simulations similar to #1 (Eklund) using surface-based analysis on both thickness and fMRI. I'll prepare a report of the results, but the early indications are that the same effect is in play, though it does not look like the effects are as bad as in Eklund. For thickness ana

Re: [Freesurfer] brain mask and T1 are not the same size

2016-08-02 Thread Douglas N Greve
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/filed

Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

2016-08-02 Thread Douglas N Greve
hanks for help. >> >> > > 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 Partne

Re: [Freesurfer] brain mask and T1 are not the same size

2016-08-03 Thread Douglas N Greve
u can reach the person managing the list at >> freesurfer-ow...@nmr.mgh.harvard.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Freesurfer digest..." >> >> > >> Today's Topics: >

Re: [Freesurfer] Anonymizing FreeSurfer files

2016-08-03 Thread Douglas N Greve
> > > ___ > 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] mri_label2label

2016-08-03 Thread Douglas N Greve
_label2label before creating a mask for ROI surface based analysis > using GLM dods? Thanks > Best, > Paul > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] brain mask and T1 are not the same size

2016-08-03 Thread Douglas N Greve
;> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Freesurfer digest..." >> >> >> Today's Topics: >> >> 1. Re: brain mask and T1 are not the same size (Isabelle Des

Re: [Freesurfer] Spearman correlation in FreeSurfer

2016-08-05 Thread Douglas N Greve
gt; Bolligenstr. 111, CH-3000 Bern 60 > Tel: ++41 0(31) 930 9599, Fax: ++41 0(31) 930 9961 > Mail: martina.papme...@puk.unibe.ch > www.puk.unibe.ch > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.

Re: [Freesurfer] How does Optseq2 arrange order of conditions?

2016-08-05 Thread Douglas N Greve
> response for Con1. > > Should I add 500 ms to the first Null? or I don’t need to anything? > > Thanks for your reading. > > Best Regards, > > Chih-Hao > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mg

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

2016-08-05 Thread Douglas N Greve
/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 ma

Re: [Freesurfer] Freesurfer Digest, Vol 150, Issue 6

2016-08-05 Thread Douglas N Greve
line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: brain mask and T1 are not the same size (Isabelle Deschamps) > 2. Re: Coordinates in TRACULA group analysis (Anri WATANABE) > 3. Re: mappin

Re: [Freesurfer] Problems with QDEC

2016-08-05 Thread Douglas N Greve
ould 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 (BMC

Re: [Freesurfer] white and gray matter masks

2016-08-10 Thread Douglas N Greve
reesurfer 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.nm

Re: [Freesurfer] Registration of low-resolution EPI time series to CVS MNI (avoiding resampling)

2016-08-10 Thread Douglas N Greve
way, I am using Freesurfer 5.3. > > Your help is very much appreciated, Thanks, > > Heidi > > > > Heidi Gröhn, PhD > > CMRR > > University of Minnesota > > > > > > ___________ > Freesurfer maili

Re: [Freesurfer] resample structural ROI in functional space?

2016-08-10 Thread Douglas N Greve
text of the email, this email is not intended to form a binding > contract - a list of authorised signatories is available from the > Bangor University Finance Office. > > > > ___________ > Freesurfer mailing list > Freesurfer@nmr.mgh.

Re: [Freesurfer] query about the "normal range" in aseg.stats

2016-08-10 Thread Douglas N Greve
_ > 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] aseg.stats data output

2016-08-10 Thread Douglas N Greve
8 \ >--tablefile aseg.vol.table > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-74

Re: [Freesurfer] Problems with QDEC

2016-08-10 Thread Douglas N Greve
ible 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. >

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

2016-08-10 Thread Douglas N Greve
i_glmfit-sim after mri_mcsim. correct > Best, > Paul > > Sent from my BlackBerry 10 smartphone. > Original Message > From: Douglas N Greve > Sent: Friday, August 5, 2016 11:49 AM > To: freesurfer@nmr.mgh.harvard.edu > Reply To: Freesurfer support list > Subject:

Re: [Freesurfer] Inquiries about QDEC inflated surface

2016-08-10 Thread Douglas N Greve
___ > 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] FS V6.0 GTM PVC ROI definition

2016-08-10 Thread Douglas N Greve
using centrum semiovale as reference region. Is > there a way I can save the unsegmented white matter [5001& 5002] > during the gtmseg step or what would be its equivalent label in > the gtm_pvc results table? > > Thanks, > Pradeep > > On Thu, Jul 7, 20

Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR

2016-08-10 Thread Douglas N Greve
e - compared to running recon-all -autorecon3 with the FLAIR >> after running recon-all -all with only the T1? >> >> 4) I've also thought about using the lesion segmentation toolbox for >> SPM and completely avoid manual editing - is this preferable to using

Re: [Freesurfer] myaparc

2016-08-10 Thread Douglas N Greve
line? > > On 8/3/16 6:00 AM, Caroline Beelen wrote: > > > > > > > > > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/

Re: [Freesurfer] Qdec Generate Stats Data Table Error

2016-08-10 Thread Douglas N Greve
; > > > ___ > 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: 617-7

Re: [Freesurfer] bbregister problem in FS5.1

2016-08-10 Thread Douglas N Greve
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf

Re: [Freesurfer] Error with qdec

2016-08-10 Thread Douglas N Greve
me with this? > > Best Regards, > Mahtab. > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Cent

Re: [Freesurfer] Assessing local correlations across 2 modalities

2016-08-10 Thread Douglas N Greve
Elijah > > -- > > Elijah Mak > > PhD Candidate *|* Psychiatry > > University of Cambridge > > Trinity College, Cambridge, CB2 1TQ > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] FS V6.0 GTM PVC ROI definition

2016-08-10 Thread Douglas N Greve
Use the pet2bbpet.lta in the aux folder. If you add --no-reduce-fov, it will not change the FoV of the output image On 08/10/2016 06:06 PM, Pradeep wrote: > Its in PET native space. > > On Wed, Aug 10, 2016 at 2:55 PM Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wr

Re: [Freesurfer] Retinotopy questions

2016-08-10 Thread Douglas N Greve
is? > > Thanks very much for the help. > > Xiaomin > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358

Re: [Freesurfer] how to run correlation analysis between cortical thickness and cognitive function

2016-08-11 Thread Douglas N Greve
c? > Best regards, > Yawu > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Pho

Re: [Freesurfer] Recon-all

2016-08-12 Thread Douglas N Greve
esurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > ___ > Frees

Re: [Freesurfer] repost aseg.mgz error

2016-08-12 Thread Douglas N Greve
ogy Graduate Program > University of Southern California > jal...@usc.edu <mailto:jal...@usc.edu> > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

Re: [Freesurfer] Subject: Re: Zero cortical thickness

2016-08-16 Thread Douglas N Greve
> 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] Bad Coregistration - Left-Right Reversed

2016-08-16 Thread Douglas N Greve
Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > ___________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Do

Re: [Freesurfer] malloc_error_break/ can't allocate region

2016-08-16 Thread Douglas N Greve
__ > 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] Subject: Re: Zero cortical thickness

2016-08-16 Thread Douglas N Greve
which ROIs are coming up zero? Have you looked at the area maps for that subject for that ROI? On 08/16/2016 01:16 PM, A Nunes wrote: > I mean the area of an ROI > > On Tue, Aug 16, 2016 at 6:59 AM, Douglas N Greve > wrote: >> please include previous correspondence. Do you

Re: [Freesurfer] malloc_error_break/ can't allocate region

2016-08-16 Thread Douglas N Greve
That sounds fishy. I would use the 5.3 or 6.0 version. On 08/16/2016 03:51 PM, miracle ozzoude wrote: > FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked. > > On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > >

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

2016-08-16 Thread Douglas N Greve
__ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 &

Re: [Freesurfer] malloc_error_break/ can't allocate region

2016-08-17 Thread Douglas N Greve
out uninstalling FS > 5.1? > > Sent from my BlackBerry 10 smartphone. >Original Message > From: Douglas N Greve > Sent: Tuesday, August 16, 2016 4:01 PM > To: freesurfer@nmr.mgh.harvard.edu > Reply To: Freesurfer support list > Subject: Re: [Freesurfer] malloc_erro

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

2016-08-17 Thread Douglas N Greve
ausing the > coreg to fail or how to fix it. > > -Afsana > > > 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, Aug

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

2016-08-17 Thread Douglas N Greve
, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > 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, August 17, 2016

Re: [Freesurfer] Structural group analysis

2016-08-22 Thread Douglas N Greve
ay to solve > this problem. > > > Please let me know if my problem is incomprehensible! > > > Best, Silas > > > > _______ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D.

Re: [Freesurfer] $SUBJECTS_DIR

2016-08-22 Thread Douglas N Greve
s.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

Re: [Freesurfer] Recon-all Correcting Defect 0

2016-08-22 Thread Douglas N Greve
list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.har

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