in .mgz format using mri_vol2surf
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve
>> mailto:gr...@nmr.m
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harva
ind reply would be appreciated.
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
ea of the white surface because that will be independent of changes in
thickness.
> Thank you in advance.
>
> Best regards,
> Ting
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destroy the material in its entirety, whether electronic or hard copy.
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eveland Clinic is ranked as one of the top hospitals in America by U.S.News
> & World Report (2015).
> Visit us online at http://www.clevelandclinic.org for a complete listing of
> our services, staff and locations.
>
>
> Confidentiality Note: This message is intended for use only by the
> individual or
.mgh.harvard.edu/mailman/listinfo/freesurfer
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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MGH-NMR Center
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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ted
> cluster defining threshold of p<0.005) in the contrast that was
> designed for that test?
>
> Regards
>
> MV
>
> On Wed, Oct 12, 2016 at 10:27 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> try this binary
0.59810 -1.0287286/
>> / powell nthiter 3: fret = -1.028729/
>> /#@# 2 867 3.12259 15.49539 68.16066 7.07157 0.0
>> 0.59788 -1.0287287/
>> /Powell done niters total = 4/
>> /OptTimeSec 161.2 sec/
>> /OptTimeMin
gnosis Douglas. How could I get the voxel sizes
> right from input nifti pet and mri data ?
>
> Best regards,
> Matthieu
>
>
> Le 12 oct. 2016 10:05 PM, "Douglas N Greve" <mailto:gr...@nmr.mgh.harvard.edu>> a écrit :
>
> The problem appears to be th
ipts/Two
> Best Regards
>
>
> F.Keyvanfard
>
>
>
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se, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
>
>
>
> __
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>
>
> Thanks
> Vasudev
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harva
Thank you for any help!
> Bests,
> John
>
>
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MGH-NMR Center
gr...@nmr.mgh
>
> 2) Is there a way to input my own estimation of ventricular CSF signal
> to mri_gtmpvc?
>
> Thanks!
> Adam
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu
but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
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Linux v5.3.0
>
> any help would be greatly appreciated.
>
> Brian
>
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Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
ET as
> planned. If it is -- is there a way to expose the CSF estimation in
> the script so that I could input my own estimation (just the ventricles)?
>
> Thanks!
> Adam
>
> On Thu, Oct 20, 2016 at 3:24 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> w
DoPBSubmit = 0
> DoBackground = 0
> DiagCluster = 0
> gd2mtx = dods
> fwhm = 10.682767
> ERROR: cannot find
> /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd
> I smoothed just fwhm = 1
> Kindly how can I troubleshoo? thank you for any advic
sity of Bonn
> ..
> Sigmund-Freud-Str. 25
> 53127 Bonn
> ..
> bastian.da...@ukb.uni-bonn.de
> www.epileptologie-bonn.de
>
>
> ___________
> Freesurfer mailing lis
gt;> ___
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>>
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Permission denied.
>
> Is there an updated link that I can use to download it?
>
> Daiana
>
>
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this
las from scratch could I
>> input that in the interhemispheric registration analysis?
>>
>> The ROIs for the diffrerent regions per hemisphere are 50-100
>> vertices
>>
>> On Oct 24, 2016 5:03 PM, "Douglas N Greve"
>> mai
hing obvious about the command usage...
>
> —•—
> Chiara Giacosa
> PhD student
> Concordia University
>
>
>> Il giorno 01 nov 2016, alle ore 12:47, Douglas N Greve
>> ha scritto:
>>
>> what do you mean "it does nothing" ?
>>
>>
>
fsaverage_sym template the L/R
>> vertices do not correspond to one another. So will it be possible to
>> flip the analysis values and template in order to perform LH v RH
>> comparisons at the group level?
>>
>> System: Linux CentOS 6 x86_64 (64b) stable v5.3.0
>>
>&
aking was hardly
> necessary after that. It truly works wonders :)
> Best Wishes,
> Elijah
>
>
>
>
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view, the values are either 0 or
> 255 (see attached image). However, they
> were binary (0 or 1) in the label_aalf.mnc input file...
>
> Trisanna
>
>
> --
> Ph.D. CandidateMcGill University
>
> Inte
eem
> to be a straight answer.
>
> Thank you,
> Daiana
>
> On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> I've written a script that will come out with version 6, but I've
> put it
> her
ust follow the instructions on the xhemi page
>
> Thank you!
> Daiana
>
> On Tue, Nov 1, 2016 at 5:22 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> You can certainly get the lh and rh ROI stats in table form and
> then do
>
;
> Thank you,
>
> Daiana
>
> On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> I've written a script that will come out with version 6, but I've
> put it
> here
>
> https://gat
unknown
>
> Thanks very much,
>
> Gabriela HOSSU
>
>
>
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Douglas N. Greve, Ph.D.
MGH-NMR Ce
fsgd.dat
> --C 2G0C.mtx --glmdir subc.glmdir
> DoSim = 0
> UseCache = 1
> DoPoll = 0
> DoPBSubmit = 0
> DoBackground = 0
> DiagCluster = 0
> gd2mtx = dods
> fwhm = 10.682767
> ERROR: cannot find
>
> /usr/local/freesurfer/s
As I mention above, it
will not necessarily sample WM, and that probably invalidates it somewhat
>
> Many Thank!
>
> Mohamad
>
>
>
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> http
seg flag for other commmands. I built a cortical Atlas and dont
> have subcortical labels
>
> Thank you ,
> Daiana
> Daiana Pur
>
>
>
>
> On Wed, Nov 2, 2016 at 2:48 PM -0400, "Douglas N Greve"
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
nalysis and setting GLM for thickness and
> age.
> How could I do that with the results of xhemi for asymmetry in left
> and right hemisphere?
>
> Thank you for you help!
>
>> On Nov 4, 2016, at 10:31 AM, Douglas N Greve
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
&
e-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Friday, November 4, 2016 10:29 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_preproc
>
>
>
> On 11/04/201
rfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Friday, November 4, 2016 12:09 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_preproc
>
> Do you have a question about the image?
>
>
> O
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
bel...
> MatrixMultiply: m2 is null!
>
> --
>
> And then tksurfer closes. I'm not sure why this is happening -- any
> help would be greatly appreciated!
>
> Thanks,
> Sophie
>
>
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t;
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Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726
the surfaces themselves?
>
> Anyways, this makes me think that I can't automate finding the GM, and
> I would rather go from LUT numbers, and hence the above question.
>
> Thanks,
> pt
>
>
>
> ___
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gt; Writing to
> /data-01/trisanna/freesurfer/fsaverage/committee_meeting/DISPLAY_overlays_fsaverage_left/aalf_lh/mri_concat_test.mgz
>
>
> thanks
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
.
>
> Do you mean you do not see the binary values on your end?
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Mon, Nov 7, 2016 at 3:53 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard
map?
>
> Thanks!
> Mihaela
>
> On Mon, Nov 7, 2016 at 3:16 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Run mri_glmfit-sim using the Qdec output folder as the --glmdir and
> setting the thresholds and signs as you had them in qde
I might not have used the right word. Let's say 'blob'
> instead of cluster. It's something like the plot attached. Each
> circle/square is a subject. I would like to export that so I can make
> the plot myself.
> Best,
> Mihaela
>
> On Mon, Nov
r mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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://g
ieve this e-mail was sent to you in
> error and the e-mail contains patient information, please contact
> the Partners Compliance HelpLine at
> http://www.partners.org/complianceline
> <http://www.partners.org/complianceline> . If the e-mail was sent
>
hed.
> Could you give me suggestions how to trouble shoot the problem.
> Thank you!
> Lauri Tuominen
>
>
>
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ution or disclosure by others is strictly
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>
>
>
> _____
coordinates
>
> Pruning by CW P-Value 0.05
>
> ERROR!
>
> Error in Monte Carlo simulation: Error running mri_surfcluster!
>
> Many thanks for your help.
> Best Wishes,
> Elijah
>
>
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&g
gm option on
>>>>>> aparc+aseg.mgz This uses some rules to
>>>>>> determine what is GM and creates a mask
>>>>>> of GM. You can then feed this into
>>>>>>
al_stats for
> individual subjects?
>
> Thank you,
>
> Daiana
>
>
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M
ipient), please contact the sender and delete all copies of the message.
> Thank you.
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>
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MGH-NMR Center
gr...@nmr.mgh.harvard.ed
t;
>
> Writing results
> C_pvr_cth
> maxvox sig=4.6783 F=34.7936 at index 31050 0 0 seed=1479612145
> mri_glmfit done
>
> Thanks a lot for your help.
>
> Best Wishes,
> Elijah
>
>
>
> ___
> Freesurfer mailing l
gt;
> Thanks again. Really appreciate your help!
>
> Best Wishes,
> Elijah
>
>
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d how) comands I have to use?
>
> Thanks in advanced!
>
> Cheers.-
>
> Stella
>
>
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Douglas
or the last couple days,
> any insight would be appreciated.
>
> Eli
>
> On 11/09/2016 05:51 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>> Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N Greve
>> Subject: Re: [Freesurfer] mri_convert
>> slope scale T
Area_mm2 but Mean in first way gives me (8.8194+10.3661+10.3365)/3
> = 9.84066 and with .label file Mean = 8.9637.
>
> Did I have miss anything and how is computed mean intensity ?
>
> Many thanks in advance.
>
> Best regards,
> Matthieu
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugRepor
t; > it is addressed. If you believe this e-mail was sent to you in
> > error and the e-mail contains patient information, please
> contact
> > the Partners Compliance HelpLine at
> > http://www.partners.org/complianceline
> <http
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs:
t, dcm2nii does not apply the scale either, however, it copies
> over the slope scale header entry, enabling other software (eg
> Freeview..) to apply the scaling..
>
> Hope this clarifies. Thanks for checking into this.
>
> On 11/10/2016 12:18 PM, Douglas N Greve wrote:
>> So
gt;
> Best,
> Chris
>
> On Thu, Nov 10, 2016 at 10:26 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> You can use mri_concat to create a stack of overlays, then
> mri_surf2surf
> the entire stack, then split the stack.
>
>
>
SrcMultiHits
> = 4.69815
> Saving target data
> Saving to /tmp/out.mgh
>
> real16m25.129s
> user16m24.160s
> sys 0m0.260s
>
> On Thu, Nov 10, 2016 at 11:40 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Years ago I used
ras to voxel transform:
> -1. -0. -0. 81921.
> -0. -0. -1. 0.5000
> -0. 1. -0. 0.5000
> -0. -0. -0. 1.
>
>
> On Thu, Nov 10, 2016 at 12:34 PM, Douglas N Greve
> mailto:gr
ella
>
>
> --
> Sánchez, Stella M.
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs
John
>>
>>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number
kr2scanner give me then?
>
> Thanks - Don
>
>
>
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Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nm
oxels is
> equal to NVertices and Volume_mm3 is equal to SurfaceArea_mm2 ?
>
> Best regards,
> Matthieu
>
>> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte
>> mailto:matthieuvanhou...@gmail.com>> a
>> écrit :
>>
>> Thank you Douglas !
>>
>>
>> Le 10 nov.
ould have been done on different scanners?
>
> Don
>
>
> 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: Friday, November 11, 201
: talairach_afd: Talairach Transform: transforms/talairach.xfm
> ***FAILED*** (p=0.0386, pval=0.0034 < threshold=0.0050)
> INFO: Attempting MINC mritotal to perform Talairach align
> Do I need to warry about this error? I appreciate any suggestion to
> improve analyzing this image.
&
Best regards,
> Matthieu
>
>
> Le 11 nov. 2016 9:21 PM, "Douglas N Greve" <mailto:gr...@nmr.mgh.harvard.edu>> a écrit :
>
> NVox is the number of vertices. The Volume_mm3 is not meaningful.
> Do you
> want area?
>
>
> On 11/11/
t; area ?
>
> Best,
> Matthieu
>
>
> Le 11 nov. 2016 10:55 PM, "Douglas N Greve" <mailto:gr...@nmr.mgh.harvard.edu>> a écrit :
>
> If you want to do it on fsaverage, then
>
> mris_segstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.a
tes, did its thing, and then
> picked the T1 to provide the tkr2scanner transform.
> ???
>
> Don
>
>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
>> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
fslswapidim. What is
> your choice in this case? I highly appreciate your experience !
> Bests,
> John
> *Sent:* Friday, November 11, 2016 at 4:42 PM
> *From:* "Douglas N Greve"
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] recon all
> On this
.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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your help.
>
> Best,
> Hamdi
>
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.
ridge
>
> Trinity College, Cambridge, CB2 1TQ
>
>
>
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MGH-NMR Center
gr..
vertices or
> surface area ?
>
> Best,
> Matthieu
>
>
> Le 11 nov. 2016 11:33 PM, "Douglas N Greve" <mailto:gr...@nmr.mgh.harvard.edu>> a écrit :
>
> Vertices do not have equal areas and are not equally spaced
>
>
> On 11/11/2016 05:11 P
bject and apply the registration to the PET first
> registered onto native space ? In this case, how and where is this
> transformation has been saved ?
>
> Best regards,
> Matthieu
>
> 2016-09-30 23:05 GMT+02:00 Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>>
advance,
> Foteini.
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Numbe
Rigid.
On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote:
> Still using rigid-body registration on --long subject directory ?
>
> Or is affine registration in this case needed ?
>
> Best regards,
> Matthieu
>
> 2016-11-14 17:12 GMT+01:00 Douglas N Greve <mailt
Dear Douglas,
>
> As I am working on fsaverage with statistical maps, I supposed they
> are smoothed ?
>
> Do I still have to weighting by area ?
>
> Best regards,
> Matthieu
>
> 2016-11-14 17:08 GMT+01:00 Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>>:
&
You can use fscalc to multiply the pet and area maps,eg
fscalc pet.lh.nii.gz mul lh.white.avg.area.mgh -o weighted.nii.gz
On 11/14/2016 11:53 AM, Matthieu Vanhoutte wrote:
> Ok I will try both.
>
> Best,
> Matthieu
>
> 2016-11-14 17:50 GMT+01:00 Douglas N
e <http://med.uni-muenchen.de>
> <mailto:dominic.dw...@med.uni-muenchen.de>
>
> T: +49 (0)89 4400 55880
>
>
>
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Hi, I just found a bug in mri_glmfit-sim in regards to GRF on
volume-based data. I put a fixed version at the same location. Please
use the new version
On 11/04/2016 10:25 AM, Douglas N Greve wrote:
> oops, sorry,
>
> download these files
>
> https://gate.nmr.mgh.harvard.edu/
s to label...
> MatrixMultiply: m2 is null!
>
> --
>
> And then tksurfer closes. I'm not sure why this is happening --
> any help would be greatly appreciated!
>
> Thanks,
> Sophie
>
>
>
> _____________
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>
>
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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
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>
>
>
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
d.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+Extracting+structural+measures+from+trend%5C-level+PET+clusters%22&o=newest>
>
> Douglas N Greve
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22>
>
> Mon, 14
gt;> to be copying over or applying the scale for either modality.
>>
>> On 11/10/2016 12:40 PM, Douglas N Greve wrote:
>>> What is the dicom tag for the scale?
>>>
>>>
>>> On 11/10/2016 01:29 PM, Rockers, Elijah D. wrote:
>>>> As far as
gt;
> So I presume I am going to come across the same problem with the images
> reregistered to fsaverage_sym if I do the analyses like you suggested?
>
> How can I proceed using isxconcat without rerunning the 1st level analyses in
> the average template spaces?
>
>
> T
rchemi lh --srcsurfreg
> sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg
> --sval fMRI.mgh --tval fMRI305.mgh--sfmt curv --noreshape --no-cortex
>
>
>
>
>
>
> _______
> Freesurfer mailing list
> Fre
ture on how to correct for
> multiple comparisons using clusters of ROIs on surface would be
> appreciated?
>
>
> Thank you,
>
> Erik Jahner
>
>
>
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>
in
> a group?
>
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+Comparing+z+score+maps+between+2+modalities+in+a+group%5C%3F%22&o=newest>
>
> Douglas N Greve
>
> <http://www.ma
s for your help.
>
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