> 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.
Linux 7.1 with 48 core
> memory.
>
> I was wondering if you could possibly provide any advice for
> troubleshooting this error.
>
> Best wishes,
> Vasiliki
>
>
>
>
>
>
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> https://mai
he volume of the hippocampus?
> I and very looking forward to hearing from you.
>
> Yours sincerely,
> Junji Komatsu
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ats
>
> for writing//
> //Errno: No such file or directory/
>
>
>
> Thanks a lot in advance,
>
> Regards,
> Subin
>
>
>
> ___________
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ce.
>
> Shads
>
>
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>
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> Scotland, with registration number SC005336.
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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
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
> > > >
>
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>
>
>
>
>
> __
did not make
much of a difference.
doug
>
>
> Thanks,
> Pradeep
>
>
>
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MGH-NMR Center
gr...@nmr.mgh
gt;
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs:
; * 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
er mailing list
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> 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
ndidate
>
> Department of Radiology
> Center hospitalier universitaire vaudois (CHUV) and Université de
> Lausanne (UNIL)
> Rue du Bugnon 46, CH-1011
>
>
>
>
>
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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/B
t;
> Error in write_surf (line 38)
> fwrite3(fid, TRIANGLE_FILE_MAGIC_NUMBER);
>
>
> *
> thank you in advance for your help!
> Dulce*
> *
>
>
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> https
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
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
f Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
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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
>
> -
LUT.txt
> --subject SUBJECT_ID --brainmask mri/brainmask.mgz --brain-vol-from-seg
>
>
> Thanks very much for your help!
>
> Best,
> Hamdi
>
>
>
>
>
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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
>
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
> 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
>
&
__
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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/Bu
l Research Coordinator
> Stufflebeam Lab
> Athinoula A. Martinos Center
> Massachusetts General Hospital
> 149 13th Street, Room 1115S
> Charlestown, MA 02129
>
>
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> Freesurfer@nmr.mgh.harvard.ed
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
>
file view in
> Freeview) are exactly the same. Would you please guide me with this?
>
> Best Regards,
> Mahtab.
>
>
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eq2 in the right way? How could I fix it?
> Thanks in advance & Best regards,
> Feng Zhou
>
>
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--
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
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
&
.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?
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:
>>
>>
> 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/
>
>
>
>
>
>
>
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]
> 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
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-72
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
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,
>
>
ion
>> and Technology
>> Karolinska University Hospital | Department of Radiology
>>
>>
>
>
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1.776 2015/12/17 18:09:34 fischl Exp $
>
>
>
> ___________
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@
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
, 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..
rfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
&g
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
>
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!
>>>
>>
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
>
>
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> https
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
.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
>
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
_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
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
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,
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
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
; 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
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
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
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
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
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:
>
>
>
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Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax
_label2label before creating a mask for ROI surface based analysis
> using GLM dods? Thanks
> Best,
> Paul
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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;>
>> 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
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
>
>
>
>
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> https://mail.
> 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
>
>
>
> ___
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/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
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
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
reesurfer mailing list
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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.nm
way, I am using Freesurfer 5.3.
>
> Your help is very much appreciated, Thanks,
>
> Heidi
>
>
>
> Heidi Gröhn, PhD
>
> CMRR
>
> University of Minnesota
>
>
>
>
>
> ___________
> Freesurfer maili
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.
>
>
>
> ___________
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> Freesurfer@nmr.mgh.
_
> Freesurfer mailing list
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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:
8 \
>--tablefile aseg.vol.table
>
>
> ___
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Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-74
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.
>
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:
___
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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: s
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
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
line?
>
> On 8/3/16 6:00 AM, Caroline Beelen wrote:
>
> >
>
> >
>
> >
>
> >
>
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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me with this?
>
> Best Regards,
> Mahtab.
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MGH-NMR Cent
Elijah
>
> --
>
> Elijah Mak
>
> PhD Candidate *|* Psychiatry
>
> University of Cambridge
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> Trinity College, Cambridge, CB2 1TQ
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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
is?
>
> Thanks very much for the help.
>
> Xiaomin
>
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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Phone Number: 617-724-2358
c?
> Best regards,
> Yawu
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Pho
esurfer mailing list
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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
Room 2612
> Charlestown, MA 02129
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> Fax: 617-726-4078
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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/fs
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
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:
>
>
__
>> *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
&
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
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
, 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
ay to solve
> this problem.
>
>
> Please let me know if my problem is incomprehensible!
>
>
> Best, Silas
>
>
>
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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.
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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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