did you check the registration? Run mni152reg --help to see how
On 2/26/19 2:36 PM, john Anderson wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve,
>
> I used --regheader to move PET to T1.
> mni152reg in mri_vol2vol as follows:
> mri_vol2vol --mov PET.nii.gz --mni152reg --targ
>
sorry, yes, that is right
On 2/27/19 2:18 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Sorry, I just found in a previous post by doug that ADC is the same as MD?
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
>
Yes
On 2/27/19 2:00 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> There is no mean diffusivity output with dt_recon. How would you
> suggest to create MD images? Could you simply divide the adc.nii.gz
> map by 3?
>
> Best,
> *Daniel Callow*
> /PhD Student,
---
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Greve, Douglas
> N.,Ph.D.
> *Sent:* Thursday, February 28, 2019 2:41:25 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] projfrac question
&
Did you check the registration? My guess is that the registration failed
because the initial FSL registration failed. I've put a new version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/dt_recon
it has a better initializer. Just copy it over the one in
$FREESURFER_HOME/bin (make a
That looks pretty awful. You should check the orig.nofix surfaces. I bet
your data is extremely noisy
On 2/28/19 11:37 AM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
>
>
> Dear Freesurfer devs,
>
>
> I ran the recon-all in one subject and and this process was
The projfrac function might not be working in the way that you think. It
might not actually be re-running anything. Did preproc-sess finish
faster than you would have expected? You can try deleting the projfrac
output and re-running. You can also run preproc-sess with -force, but
this will
iour score.
>
> Are you are suggesting that I should put square root values of the
> behavioural scores in the design matrix? I am not sure if that is the
> right approach.
>
> Looking forward to hearing back from you.
>
> Abhinav
>
> On Wed, 20 Feb 2019, 04:12
need more info
On 2/27/19 9:42 AM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I am trying to do a registration with tkregister but am experiencing
> this type of issue:
>
>
> The image I should fit is the sagittal view instead of coronal.
>
> Is there some way to change it to coronal
to extract betas for each subject from the group analysis?
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Greve, Douglas
> N.,Ph.D.
> *Sent:* Thursday, November 29, 2018 11:19:33
it says it cannot find /XYZ/2123.nii
probably this file does not exist
On 2/28/19 10:09 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer community,
>
> when I run mri_coreg I get the following error.
> /XYZ/2123/mri/brainmask.mgz is in the specified location.
Why did you use --regheader in vol2vol? You will probably need to do a
registration (mri_coreg). Did you check the mni152 reg?
On 2/26/19 10:01 AM, john Anderson wrote:
External Email - Use Caution
Dear FS experts,
I would like to move PET image to MNI152. What is the correct command
Different OSs will often have different math libraries which can
generate different results. Usually, these are very small, but we still
recommend that all group analyses use the same platform.
On 2/25/19 5:18 AM, Tim Schäfer wrote:
> External Email - Use Caution
>
> Dear Freesurfer
e specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
> 1. Re: ?h.white does not exist (Bruce Fischl)
> 2. [All] postdoctoral position in PET imaging available at MGH /
> Martinos Center (Bruce Fischl)
> 3. Re: ?h.white does not exist (Weber,
aradigm folders generated from
> the 1-st level modelling of any subjects in the 2-nd level modelling,
> is that correct?
>
> On Fri, 22 Feb 2019 at 16:35, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> While the name of the paradigm file must
When you specify the --seg, just use gtmseg.mgz and not the whole path.
For mgx, I'd need to know what you intend to do with it. Is it a
surface-based study? If so, then I'd go with .01 in stead of .25
On 2/25/19 11:05 AM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
technically, there is not really a left and right hemisphere of
fsaverage_sym. When you register to fsaverage_sym, you register both the
left and right hemis of your subject to the "left" hemi of
fsaverage_sym. The "left" hemi atlas is made of both left and right
hemis from the subjects that
-0. 1.
Il giorno ven 22 feb 2019 alle ore 22:19 Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> ha scritto:
That looks right. Can you verify that the seg (sourcedata...) is in the
conformed anatomical space? Use mri_info can compare the output (particularly
the v
While the name of the paradigm file must be the same across runs and subjects,
the contents paradigm file can be different. That should be able to handle what
you are doing
On 2/22/19 3:42 PM, Zhi Li wrote:
External Email - Use Caution
Hello FreeSurfer experts,
It seems that all the
It depends on what you eventually want to do with it. The warning was so that
people would not go off and do, eg, correction for multiple comparisons or
something where there was some assumption about consistency between the
surface-based and volume-based results.
On 2/22/19 3:18 PM, Haroon
not running the function
correctly.
This set of regions are in the same space of the functional data but registered
to the raw T1.
Best
Francesca
Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> ha scritto:
There should be a registratio
You do not need to downsample the orig.mgz in this case
On 2/22/19 1:19 PM, Ey Dude wrote:
External Email - Use Caution
Hi all,
I would like to downsample my fsnative mesh by a factor of 0.1 and sample my
BOLD data to surface space in a next step. I have successfully downsampled my
On 2/22/19 1:47 PM, john Anderson wrote:
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Hi Dr Greve,
Yes, in my lab we normalize DPA713 tracer to whole brain mean using the command
fslmaths something like
fslmaths pet.nii -mask mask -inm 1 pet_normalized_whole_brain.nii.gz
For kinetic modeling..
you can do -autorecon2 -autorecon3 and it should work. The T2pial is done in
the middle of autorecon3. If you don't spec autorecon3, then it will skip the
initial part of autorecon3, and that is what is causing the error
On 2/22/19 1:05 PM, Bruce Fischl wrote:
no, you need to run autorecon2
sometimes the -hires flag does not work very well. For the subjects where it
does complete, do the surfaces look ok? You can also use recon-all.v6.hires
with the -conf2hires option (available in fs6 on our network).
On 2/21/19 2:36 PM, Nasiriavanaki, Zahra wrote:
Hi Bruce
Thank you very much
what do you mean the surface is still messed up in freeview?
On 2/22/19 8:58 AM, Loucao, Ricardo wrote:
External Email - Use Caution
Thanks for the reply!
I tried the --vol-geom orig.mgz option but to no avail.
Small update: I inspected the metadata on the surface files using mris_info
t 0 for the qdec version? If it is the source of the current issue, how can I
configure the Bonferroni correction? If not, do you have any idea how I can
resolve the problem?
Many thanks in advance.
Regards,
Giuliana Klencklen
[QdecGroupComparison.jpg]
On Fri, Feb 15, 2019 at 5:24 PM Greve, Douglas N.,P
That 3T18yo atlas is added when you include the -3T option (which for some
reason you did when you used -all but not -autorecon1). It is expected that
they could give different eTIVs. In the example you give below, all but the
FS5-autorecon1 were fairly close. Did you check the registrations?
See slide 47 here
https://fscph.nru.dk/slides/Emily/Copenhagen_Group_Analysis.pdf
On 2/19/19 6:07 PM, ?? wrote:
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Yes, one more question where can I get the example of mri glimfit for ROI
analysis
---Original---
From: "Greve, Douglas
N.,Ph.D."&
On 2/22/19 11:43 AM, john Anderson wrote:
External Email - Use Caution
Dear Dr Greve,
Thank you so much for the response! Indeed, I used MRTM2 for HB pathological
regions and the results were very confusing Based on your response bellow,
I understand that for pathological
qdec is not really being supported anymore. It is better if you use the command
line stream
On 2/21/19 6:22 PM, Arsenije Subotic wrote:
External Email - Use Caution
Dear Freesurfer experts,
I am having issues choosing the spc option for my QDEC two stage longitudinal
analysis as it
during the preprocessing and to apply this to each region. What's the best
procedure?
Best
Francesca
Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> ha scritto:
Yes, if you run it with the --targ as orig.mgz for the given s
See here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_freeview
On 2/21/19 3:01 PM, Daniel Davidson Callow wrote:
External Email - Use Caution
Hello,
I have run through dt_recon and want to use anatomically based segmentations
(aseg) to create ROIs for
It should have corrected surface.
On 2/22/19 3:26 AM, Matthieu VANHOUTTE wrote:
> External Email - Use Caution
>
> Dear FS's experts,
>
> In the perspective of correcting generated surfaces errors or defects,
> does the gtmseg command need corrected surfaces or could it be launch
>
that looks right to me
On 2/22/19 6:25 AM, Tim Schäfer wrote:
> External Email - Use Caution
>
> Nevermind, I think I got it to work:
>
> mri_vol2vol --mov subject_x_samples.mgz --s subject_x --targ
> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
>
On 2/22/19 7:58 AM, john Anderson wrote:
External Email - Use Caution
Hi Dr Greve,
I would like to use petsurfet to do kinetic modeling (KM), the pipeline is
straightforward and easy to use. Thank you so much! I would appreciate any
clarifications relevant to my questions bellow:
1)
On 2/21/19 12:56 PM, john Anderson wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve,
>
> Thanks for the response.
> yes, I need to extract the acquisition times for kinetic modeling
> using PET surfer. Please I have two follow-up questions and I
> appreciate any highlights:
> -
; Also, I did not find a readable file for the segmentation data. I
> tried to read the aparc.a2009s+aseg.mgz on Matlab but that didn't work.
> Show quoted text
>
> On Thu, 7 Feb 2019, 16:10 Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu> wrote:
>
> First, you'll have
inal Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve,
> Douglas N.,Ph.D.
> Sent: 14 February 2019 16:36
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Sections of Temporal Lobe not includ
When you run mris_convert try adding --vol-geom orig.mgz where orig.mgz
On 2/20/19 7:14 AM, Loucao, Ricardo wrote:
>
> External Email - Use Caution
>
> Dear FS experts and users,
>
> I’m having some troubles with CAT surfaces visualisation in
> tkregister2 and Freeview.
>
> Context: I’ve
cheers
> Bruce
> On
> Mon, 18 Feb 2019, Francesca Strappini wrote:
>
> >
> > External Email - Use Caution
> >
> > Thank you!Now the registration is better but still not perfect.
> Is there a way to improve it?
> >
>
you mean you want the acquisition times to do kinetic modeling? I don't
have anything to do that. Also, you should check to see whether your PET
has intensity scaling imbedded in the dicom as the v6 mri_convert does
not handle this properly.
On 2/20/19 11:44 AM, john Anderson wrote:
>
>
file...
> Thanks for your help,
> Vale
> ___________
> *>Greve, Douglas N.,Ph.D.*DGREVE at mgh.harvard.edu
> <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20clusters%20annotation%2
remaking my fsaverage with an older FS version to see
> if that may fix the issue.
>
> Please let me know if my questions are unclear, and I will try to
> rephrase and add script input/output.
>
> Thanks,
> Doug P
>
> -------
It is cerebral white matter, so it excludes brainstem and cerebellar white
On 2/21/19 11:14 AM, Mehndiratta, Ambica wrote:
> Hello,
>
> I am trying to extract the white matter volume based off the
> aseg.stats. I noticed the text includes "total cortical white matter
> volume" and I was
I highly recommend the multiecho mprage at about 1mm.
On 2/21/19 10:30 AM, Bruce Fischl wrote:
> Hi Mustafa
>
> FreeSurfer should work fine with many image protocols. If you have the
> freedom to choose one, Andre van der Kouwe (ccd) can point you at the
> sequence he developed for Siemens. If
It cannot. It just does simple tensor analysis. Not sure what else to use.
On 2/20/19 9:02 AM, john Anderson wrote:
External Email - Use Caution
Hi FS experts,
I would like to inquire about the command "dtrecon" in Freesurfer.
Is this command able to process multishell diffusion data?
?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Or I can not use mri to do the Glm for subcortical volume analysis ?
>
> ---Original---
> *From:* "Greve, Douglas N.,Ph.D."
> *Date:* Tue, Feb 19, 2019 21:29 PM
> *To:* "freesurfer@nmr.mgh.harvard.edu"
I have not really stressed the code with --pargs (it is a relatively new
program), but if it produces the same output, then it should work
On 2/19/19 5:01 PM, Daniel Leopold wrote:
>
> External Email - Use Caution
>
> Thank you, Doug. I'm aware of fspalm, but stayed with palm in order to
You can use mri_surf2surf or mris_apply_reg to do the transferring
On 2/19/19 4:51 PM, Bruce Fischl wrote:
> Hi Alex
>
> yes, the vertices of the lower res fsaverage representations come
> first in the ordering. So the first 12 are ico0, then the first 42 are
> ico 0 and ico 1, etc
>
>
You can create an annotation with mris_seg2annot (you basically have a
surface-based segmentation). Run it with --help to get more info
including examples. You will need to create your own color table
On 2/19/19 3:21 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I have a 3D volume mask
rh.PDDvsHC.volume.10.mgh
>
>
> Voxel Volume is 1 mm^3
>
>
> Generating list of segmentation ids
>
>
> Found39 segmentations
>
>
> Computing statistics for each segmentation
>
>
>
> Reporting on38 segmentations
>
>
> Using PrintSegStat
>
>
> Co
Not sure exactly what you mean by a template or what you would want to
do with such a thing. You can run make_average_subject to create a
folding atlas.
On 2/19/19 3:24 AM, Vivek Sharma wrote:
>
> External Email - Use Caution
>
> I'm working on source reconstruction using MEG data. For
what are the artefacts exactly? It looks like the back of the brain was
not segmented. Is there something in the raw data? Otherwise, look
though the trouble shooting tutorial.
On 2/18/19 12:19 PM, Backhausen, Lea wrote:
>
> External Email - Use Caution
>
> Dear FreeSurer experts,
>
>
Sorry, qdec is not really being supported anymore. You'll have to use
the "command line" stream (ie, creating an FSGD file, running
mris_preproc, mri_surf2surf, mri_glmfit). See the group analysis tutorial
On 2/18/19 2:21 AM, Hua, Jessica wrote:
>
> External Email - Use Caution
>
> Hi
yes, run it twice. The second time specify the output of the first run
with --merge
On 2/17/19 3:29 PM, Bruce Fischl wrote:
> sorry, I'm not sure what your question is. You probably have to run it
> twice - once for each hemi
> cheers
> Bruce
> On Sun, 17 Feb 2019, Barletta, Valeria wrote:
>
>>
see this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
On 2/16/19 6:48 PM, Daniel Leopold wrote:
>
> External Email - Use Caution
>
> Hi all,
>
> Do you have any suggestions on how I could extract stats (e.g.,
> thickness, area, LGI, etc.) from a cluster(s) identified via palm?
On 2/16/19 2:54 PM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
>
> Dear Douglas,
>
> I wanted just to compute rescaled PET image without any PVC but
> following the same process as if I would have applied PVC. Moreover, I
> didn’t want to reduce FOV with auto mask
I'm not sure what you are trying to do here. Ico7 is just a 7th order
icosahedron and does not "belong" to any subject. What belongs to
fsaverage or fsaverage_sym is the atlas of curvatures and registrations
derived from them (eg, lh.sphere.reg). It might be easier to use
mris_apply_reg
A tmap is not produced. You can get one with
fscalc gamma.nii.gz sign -o gamma.sign.nii.gz
fscalc F.nii.gz sqrt mul gamma.sign.nii.gz
doug
On 2/15/19 4:12 PM, Lauri Tuominen wrote:
> External Email - Use Caution
>
> Dear freesurfers,
> I am trying to find a t-map for my group level test.
Check the lh.orig and lh.inflated surfaces
On 2/15/19 3:34 PM, ?? wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> For more than 3 hours
>
> ---Original---
> *From:* "Greve, Douglas N.,Ph.D."
> *Date:* Fri, Feb 15, 2019 20:03 PM
>
did you analyze them with different versions of FS?
On 2/15/19 3:28 PM, Morgan Botdorf wrote:
>
> External Email - Use Caution
>
> Thanks for taking a look at the file I sent! I think I have figured
> out the issue for the most part. While it shows that there is data in
> the
what do you get when you run
ls -l /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat
On 2/19/19 8:44 AM, Daniel Davidson Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I ran a successful dt_recon and then wanted to use
>
> mri_vol2vol --mov
When you say it stopped running, do you mean that it exited or that it
kept running but nothing printed out and it did not proceed to further
steps?
On 2/15/19 12:42 PM, ?? wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> when i was
, so I can compare them to each other.
>
> Based on help, I should average runs before comparing across subjects.
> My question is how should I average runs? Should average the .dat
> files? the r values?
>
>
> Thanks
>
> Mona
>
>
>
> -------
re-run selxavg3-sess?
>
> Thanks
> Best
>
> Il giorno lun 26 nov 2018 alle ore 22:31 Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>
> And you only have partial field of view fmri data on that day? No
> whole
> brain loc
If you want to use a target other than fsaverage, then you need to
register each subject to that target (eg, with surfreg). If you have
found a problem with mris_make_subject, please document it in a separate
post.
On 2/12/19 6:38 AM, Bunting, Emma wrote:
>
> External Email - Use
It sounds like you will just need to create your own design matrix and
then feed it into mri_glmfit with --X (and not include --fsgd)
On 2/12/19 12:03 AM, Abhinav Yadav wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to do GLM analysis for cortical thickness with a
>
oun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Sent: Friday, February 15, 2019 1:56:50 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer]
00
desired_rms_height -1.00
momentum 0.90
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234
-- Original ------
From: "Greve,
how long?
On 2/15/19 2:49 PM, ?? wrote:
External Email - Use Caution
Hi
Thanks for your quickly reply, yes continue to run but not print more on
terminal anymore.
---Original---
From: "Greve, Douglas
N.,Ph.D."<mailto:dgr...@mgh.harvard.edu>
Date: Fri, Feb 1
rfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, February 14, 2019 3:37:28 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] surface cortical lesions mask --> annota
The subject surface probably changed since the last time you ran qcache and now
has a different number of vertices. Try re-running qcache for those subjects.
On 2/15/19 2:58 AM, Peters, Douglas G wrote:
External Email - Use Caution
Hi Everyone,
I'm trying to prepare my Cerebral blood
This can happen if the label is small and/or you've used a lot of smoothing. It
is better to do this kind of thing in fsaverage space rather than moving the
labels back to the individual space. If you've run mri_glmfit-sim, then it
should have created a table file (something.y.ocn.dat). This
Can you do this in two steps? First, convert the dicom to a volume format (eg,
mgz or nii.gz) with
mri_convert image001.dcm dwi.nii.gz
This may or may not create bvals and bvecs. If not, then you will have to
supply them. If they are created, look at them and make sure they are right.
Next
évr. 2019 à 21:36, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> a écrit :
>
>
>
> On 2/14/19 2:25 PM, Matthieu Vanhoutte wrote:
> > External Email - Use Caution
> >
> >> Le 14 févr. 2019 à 19:37, Gre
Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2 weighted? If so,
you should use --t2 instead of --t1 in bbregister
On 2/14/19 2:18 PM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> Hi Doug,
>
> Could you advise me about how to correctly run mri_vol2vol?
> The
Oct 10 20:06:00 PDT 2018;
> root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
>
>
> dt_recon exited with ERRORS at Thu Feb 14 16:09:17 EST 2019
>
>
>
> I am unsure why it is not reading these DICOM volumes in? They should
> be in the path I specify? Is it something to
>> 'talairach.m3z' under '/mri/transforms' and some label files end with
>> 'exvivo.label' under '/label', such as 'lh.BA1_exvivo.label' and
>> 'lh.BA1_exvivo.thresh.label'.
>>
>> Thanks and best wishes,
>>
>> Lizhi
>>
>> On Thu, 14 Feb 2019 a
http://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei
On 2/14/19 2:21 PM, Antti Cajanus wrote:
> External Email - Use Caution
>
> Hi!
>
> Few weeks ago I found the thalamic nuclei segmentation tool in Freesurfer
> development version and I had it working fine. However, I can’t find
with the setenv or
> the naming of the DICOM files?. Sorry for any questions. Any help is
> greatly appreciated!
>
> On Wed, Feb 13, 2019 at 6:30 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Yes. Can you run it with --debug with the slash in f
ey
> are in .mgh format
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Greve, Douglas
> N.,Ph.D.
> *Sent:* Thursday, February 14, 2019 3:28:44 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface cortical lesions mask
On 2/14/19 2:25 PM, Matthieu Vanhoutte wrote:
> External Email - Use Caution
>
>> Le 14 févr. 2019 à 19:37, Greve, Douglas N.,Ph.D. a
>> écrit :
>>
>>
>>
>> On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote:
>>> External Email -
not sure what you mean, can you elaborate?
On 2/14/19 2:05 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I need to extract annotation files from my cortical lesion masks
> projected to the surface.
>
> Do you know whether this is possible?
>
> Thank you,
>
> Valeria
>
>
>
bel' under '/label', such as 'lh.BA1_exvivo.label' and
> 'lh.BA1_exvivo.thresh.label'.
>
> Thanks and best wishes,
>
> Lizhi
>
> On Thu, 14 Feb 2019 at 13:43, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> did you try looking in the output to see if thos
did you try looking in the output to see if those files are actually there?
On 2/13/19 1:11 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer experts,
>
> I am trying recon-all in a SGE cluster. However, the size of of the
> results was smaller than that executed in
On 2/14/19 1:04 PM, John Absher wrote:
>
> External Email - Use Caution
>
> Hi, I realize this is fairly straightforward for most of you, but I am
> relatively new to freesurfer and want to make sure I’m proceeding
> correctly with group analysis.
>
> We have ~35 TBI subjects and a
On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
>
>
>
> Le jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> a écrit :
>
>
>
> On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote
very much.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas
> N.,Ph.D.
> Sent: Thursday, February 14, 2019 1:15 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesur
There is not something that will plug-and-play for this. But you can do
something like
cd subject/surf
fscalc lh.thickness div ETIV -o lh.thickness.etiv.mgz
where ETIV is from the aseg.stats file
Then specify --meas thickness.etiv.mgz when running mris_preproc
On 2/14/19 12:50 PM, Williamson,
t; Thanks,
>
> Matthieu
>
> On 14/02/2019 17:44, Greve, Douglas N.,Ph.D. wrote:
>> The GTM operates on regions, so you can't do trilin interp. The
>> operations that you describe below are not used in mri_gtmpvc. If you
>> are trying to get something close to what the
It is certainly possible. Are some of the clusters in abs negative?
Also, I would strongly recommend using permutation if you are using such
a low clusterwise threshold. See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
The monte carlo simulation is not valid
t;
>
> echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF
>
> tee -a
>
> echo dt_recon exited with ERRORS at `date`
>
> date
>
> dt_recon exited with ERRORS at Wed Feb 13 18:44:07 EST 2019
>
> echo "" | & tee -a $LF
>
&
nearest neighbor" instead of classical
>> "trilinear" interpolation ?
>>
>> Should it be done as well when projecting from volume to surface with
>> mri_vol2surf ?
>>
>> Best,
>>
>> Matthieu
>>
>> On 11/02/2019 17:32, Gre
hard to tell from those images what is happening. Can you send an image
with an arrow pointing to where the problem is? Putting the brain
right-side-up will be helpful as well
On 2/14/19 8:12 AM, John Mc Fadden wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I have processed two
Are you going to do an FIR analysis or are you going to assume a shape
to the hemodynamic response function? If you are assuming the shape (the
usual), then the answer to both of your questions is no
On 2/14/19 8:31 AM, Rockhill, Alexander P. wrote:
> Hello Freesurfer experts,
>
> I am
Remove the backslashes
On 2/14/19 10:15 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> My_pc$ mri_surf2vol --o 0021_thickness-in-volume.nii.gz --subject 0021
> \ --so $SUBJECTS_DIR/0021/surf/lh.white
> $SUBJECTS_DIR/0021/surf/lh.thickness \ --so
>
-6298
>
>
> On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow <mailto:ddcc2...@gmail.com>> wrote:
>
>
> Is this what you mean by no variables??
>
> dt_recon --debug --i
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> -
il.com>_
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> can you send the command line without the variables?
>
>
> On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
can you send the command line without the variables?
On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
>
> External Email - Use Caution
>
> Thanks for pointing that out! Unfortunately after making the change
>
> dt_recon --debug --i
>
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