probably easiest to use matlab. see
FREESURFER_HOME/matlab/read_annotation.m, which has an example
On 4/5/2019 11:29 AM, Gonzalo Rojas Costa wrote:
> External Email - Use Caution
>
> Hi:
>
>How can I get the different values of cortical thickness in the
> insula? Not the mean and
> total CNR = 1.540
>
>
> cheers
> Bruce
>
> On Wed, 3 Apr 2019, neuroimage analyst wrote:
>
>>
>> External Email - Use Caution
>>
>> Thanks, Dr. Greve. Where can I find the correspondence between the
>> vertices in ?h.w-g.pct.mgh and
>> th
you can get the contrast from surf/?h.w-g.pct.mgh, which you can average
over each parcellation. Not sure where you would get the noise term from.
On 4/3/19 5:23 PM, neuroimage analyst wrote:
>
> External Email - Use Caution
>
> I apologize, Dr. Fischl, that I wasnt clear.
>
> We are
Forwarded Message
Subject:REMINDER - OHBM Call for Nominations
Date: Wed, 3 Apr 2019 16:22:25 -0500
From: i...@humanbrainmapping.org
Reply-To: i...@humanbrainmapping.org
To: gr...@nmr.mgh.harvard.edu
External Email - Use Caution
Organization
pr.odd.sm5.fsaverage.lh.nii.gz' to 3D volume?
>
> Thanks,
>
> Lizhi
>
>
> On Wed, 3 Apr 2019 at 12:13, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> you mean just subcortical gray matter? You could map t
> the whole brain 3D volume fmri data by changing the subcortical mask
> in folder 'mri.2mm' to the whole brain mask, but I do not need the
> part of white matter. See if it is applicable?
>
> Thanks,
>
> Lizhi
>
> On Tue, 2 Apr 2019 at 17:32, Greve, Douglas N.,P
> On 4/2/19, 3:34 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Greve, Douglas N.,Ph.D." dgr...@mgh.harvard.edu> wrote:
>
> Can you run it with --debug as the first option, capture the terminal
> output, and send it to me?
>
> On 4/2/19
On 4/2/19 4:23 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I would like to transform the task-based surface data to volume. May I
> know if it is applicable? I tried "mri_surf2vol --o test.nii.gz
> --subject sub002 --so fs/sub002/surf/lh.white
>
> Sara Sims
>
> Graduate Research Fellow
>
> University of Alabama at Birmingham
>
> Department of Psychology
>
> 205-975-4060
>
> sno...@uab.edu
>
> *From: * on behalf of "Greve,
> Douglas N.,Ph.D."
> *Reply-To: *Freesurfer support lis
It is having problems reading both the bvals and the bvecs
On 4/2/19 9:34 AM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am running dt_Recon with the following specifications and am running
> into this issue? I wasn't running into this issue previously. Two
>
Hi Antonin, I think this is a bug. Can you send me the recon-all.log file?
thanks
doug
On 4/1/19 5:49 PM, Antonin Skoch wrote:
>
> External Email - Use Caution
>
> Dear experts,
>
> I noticed suspicious values of segmentation volume in aseg.stats in
> subjects processed with version 6,
In addition to the annotation, there is a surface segmentation ("seg") that is
also produced by mri_glmfit-sim. You can convert the seg to an annotation by
using mris_seg2annot, which will take a color table that you supply. Run it
with --help to get more info.
On 4/1/2019 1:24 PM, Arsenije
er-atlas/>. And
> subject_t1.nii.gz is the subject's T1-weighted nifti file. Is there an
> easy way to check the respective geometries?
>
> Thanks again,
> JD
>
> On Mon, Apr 1, 2019 at 8:56 AM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
>
Not sure what is going on here. What is lh.atlas.mgz? Is is a surface overlay?
What is subject_t1.nii.gz? If it is not the same geometry of lh.atlas.mgz, then
strange things will happen when you do it a second time.
On 3/31/2019 12:28 PM, JD Knotts wrote:
External Email - Use Caution
Department of Psychology
205-975-4060
sno...@uab.edu<mailto:sno...@uab.edu>
On 3/29/19, 10:05 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Greve, Douglas
N.,Ph.D."<mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.>
&
What is fICL161363_06_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii ? In general,
you should not give mri_coreg a reference when using --s unless it is the same
geometry as the orig.mgz
On 3/29/19 11:55 AM, ?? wrote:
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Hi developers,
I am using the petsurfer
. 2019 om 10:58 schreef Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>:
what program generated the error? What is the full command line for that
program?
On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote:
External Email - Use Caution
Dear,
I encountered a problem when goin
r.
>
> Sara Sims
> Graduate Research Fellow
> University of Alabama at Birmingham
> Department of Psychology
> 205-975-4060
> sno...@uab.edu
>
> On 3/19/19, 3:30 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Greve, Douglas N.,Ph.D." dgr...@mgh.h
what program generated the error? What is the full command line for that
program?
On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote:
External Email - Use Caution
Dear,
I encountered a problem when going from pmod to freesurfer.
I made Vt images in pmod using the logan plot, then I
What threshold are you using in tksurfer? It should be the same as -log10(cwp),
where cwp is the --cwp threshold you used in mri_glmfit-sim. If it is
different, then it might not show all the cluster
On 3/29/19 6:48 AM, Giuliana Klencklen wrote:
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Hi FS
There is not a way to do this. Instead, try a paired analysis
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
On 3/28/19 8:08 PM, brain health wrote:
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What is the best way to run a whole- brain Group (intervention group, control
group) x Time (Pre,
It looks like the dicom file is the localizer/scout. It is not the
anatomical (eg, only 3 slices). You can try running dcmunpack to get a
list of runs in the dicom folder. Then pass one of the dicoms from the
anatomical to recon-all
On 3/27/19 4:50 PM, Z Hessam wrote:
>
> External
no, not really. You can use multiple --replace optoins, eg, --replace
-117 2 --replace -118 2 ...
On 3/27/19 6:08 PM, Song, Da-Yea wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I have a set of binary mask files that I’m trying to assign different
> values to. Currently I’m
Usually, an intensive study is done with any new tracer in which they do
arterial sampling and apply various kinetic models to determine which
one fits best (including which regions to use for high binding in
MRTM2). You should find this study for your tracer. For FDG, MRTM2 is
not appropriate
al, sagittal or else? Thank you in advance.
>
> Yours faithfully,
>
> Mustafa M. Amin
> Consultant Psychiatrist in Biological Psychiatry
> Department of Psychiatry
> Faculty of Medicine
> Universitas Sumatera Utara
>
>> On 22 Feb 2019, at 00.10, Greve, Douglas N.,Ph.
basically yes. The full instructions for a paired analysis are here
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
On 3/26/19 5:56 PM, Arsenije Subotic wrote:
>
> External Email - Use Caution
>
> Sorry,
>
>
> I was actually able to compile a FSGD file that has a single line for
You should read up on the MRTM2. Basically, when you run MRTM1, it
computes a separate k2 for each voxel eventhough the k2 should be the
same across the entire brain (since it actually refers to the reference
region). With MRTM2, you estimate the single k2 value from high binding
regions.
On
No, not easily. You could edit fmri_hemodyn.m, fast_fslgamma.m, or
fast_spmhrf.m to return your own HRF and then specify the proper one in
mkanalysis.
On 3/26/19 11:34 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer's experts,
>
> I would like to use
other advice?
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Greve, Douglas
> N.,Ph.D.
> *Sent:* Monday, March 25, 2019 11:06:53 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Free
for replying. Anything I should watch out for when using it for Tau
processing?
Thanks.
Best,
Paul
On Mon, Mar 25, 2019 at 11:19 AM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
It is certainly good for FDG. Tau is a little trickier, but I think it has been
used. I think the ref
It is certainly good for FDG. Tau is a little trickier, but I think it has been
used. I think the reference region for tau is still an open question. For FDG,
people often use pons.
On 3/25/19 10:33 AM, miracle ozzoude wrote:
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Hello FreeSurfer,
I would
sorry, it cannot be used for rats and mice
On 3/25/19 4:02 AM, 陈天鸿 wrote:
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Dear Professor:
In my study ,I want to compare the difference and similarity between the sulci
on the brains of rats and mice. I hope to use Freesurfer to acquire and compare
some
About once a year we get an email like this saying that there are inconsistent
results between SPSS and mri_glmfit. I think the problem usually boils down to
having a different design matrix. Can you extract the design matrix from SPSS
and compare it to Xg.dat? Or can you import Xg.dat and use
The intensity is partially what VBM is picking up, so it is not at all
unreasonable to look at.
On 3/21/19 9:52 PM, Bruce Fischl wrote:
Hi Dorothy
yes, we have looked at intensity effects in the gray matter before (David Salat
for example has done this). It certainly reflects degree of
Try this
mri_glmfit —-table V1_lh_stats.txt —-fsgd glm/gender_age.fsgd dods —-C
lh-Avg-thickness-age-Cor.mtx --glmdir lh.V1_gender_age.glmdir
You would only use --surface if the input is a surface map (not when the input
is a table, even if the table has data derived from the surface)
On
.harvard.edu/filedrop2/?p=65zt2jk45ll
>
> Thanks!
>
> Sara Sims
>
> Graduate Research Fellow
>
> University of Alabama at Birmingham
>
> Department of Psychology
>
> 205-975-4060
>
> sno...@uab.edu
>
> *From: * on behalf of "Greve,
> Douglas N.,Ph.D.&q
cific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
> 1. mris_preproc not running (Sims, Sara A (Campus))
> 2. Longitudinal QDEC (AKUDJEDU, THEOPHILUS)
> 3. Re: mris_preproc not running (Greve, Doug
I've put a new version of mri_glmfit-sim here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim
This should run, though I'm not 100% sure this is the right way to do it.
Let me know how it goes
On 3/19/19 10:58 AM, Victor Montal wrote:
> External Email - Use Caution
>
>
a paired t is probably fine. See
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
On 3/19/19 11:20 AM, Jose Pineda wrote:
>
> External Email - Use Caution
>
> Dear all,
>
> Im currently running a cortical thickness longitudinal analysis on a
> group of 50 patients. The
... but know that the dev version is not fully tested -- there may be
significant bugs that will not be uncovered until it is tested. As such, we may
not be able to support any problems you run into.
On 3/18/19 8:12 PM, Bruce Fischl wrote:
Hi Kody
there definitely are flags like this in the
Did you delete the bad registration file and re-run the registration
(preproc-sess)?
On 3/18/19 11:53 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Hi
I was checking the functional on structural data registration quality by using
the below command.
tkregister-sess -s $subj -fsd bold
are significant? Perhaps I am just missing
a key idea.
Best,
On Thu, Mar 14, 2019 at 5:11 PM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
The size of the cluster is not going to be affected by the number of
iterations (only by the threshold). Why would you think that the cluste
Hi Theo, sorry, QDEC is not really being supported anymore. Try using the
command line stream.
On 3/18/19 11:16 AM, AKUDJEDU, THEOPHILUS wrote:
External Email - Use Caution
Dear All,
I am running a longitudinal (2-time points) group cortical analysis in
Freesurfer 5.3 with Qdec.
can you send the terminal output? I realize it might be quite big. You can ftp
it to here: /autofs/space/nihilus_001/CICS/ACRsoftware/ACRcurrent
On 3/18/19 11:12 AM, Sims, Sara A (Campus) wrote:
External Email - Use Caution
Hello!
I have 786 subjects that I am trying to do a paired
They do not have any normalization applied. BTW, you should not scale the
thickness by the ICV
On 3/18/19 10:24 AM, Bunting, Emma wrote:
External Email - Use Caution
Hi Freesurfer experts,
I used a script created by ENIGMA to extract the cortical thickness values for
129 subjects that
See slide 30 here. does that work? If so, you have my permission to use it in
your publication or presentation or whatever
http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.pptx
On 3/18/19 8:33 AM, Mageshwar Selvakumar wrote:
External Email - Use Caution
Dear Freesurfer Community,
We
sorry, at one point you say that you are planning to use cognitive scores, then
in the next sentence you say you don't want to use them. How would you find an
association if you don't use them as a covariate?
On 3/15/19 1:23 PM, Arsenije Subotic wrote:
External Email - Use Caution
The eTIV is unrelated to the pial surface, so you do not need to edit to get a
good eTIV.
On 3/15/19 2:38 PM, Ryan Wales wrote:
External Email - Use Caution
Hello,
I'm using freesurfer ver 6.0.0.
If there are defects with the pial surface (i.e. the pial surface does not
cover all the
you please give details
on how we would do that? Specifically, would we need to use the command line
to run the Welch's T/F or would we extract values for each voxel and put them
into another software to conduct the Welch's T/F?
Thank you again.
Greve, Douglas
N.,Ph.D.<https://www.m
It looks like the library is not set up properly. Does freesurfer work
outside of matlab?
On 3/14/19 1:46 PM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
>
>
> Dear Freesurfer devs,
>
>
> Have you had occasion to review this error?. Could it be due to the
> gcc
Hi Zheng, qdec is not longer being supported. Use the "command line"
stream, see here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
On 3/12/19 7:47 AM, 郑凤莲 wrote:
>
> External Email - Use Caution
>
> Hi experts,
> I am using qdec software for the statistic of LGI. I
Can you send the command line with out variables and the full terminal
output?
On 3/14/19 8:48 AM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
>
> Dear,
>
>
> Apologies, this is a copy and paste error the full command was:
>
>
> #mri_gtmpvc --i
>
We don't really have a good way to do this. In theory, you could
concatenate them together and then let the motion correction fix the
misalignment, but I could imagine it would create some problems.
On 3/14/19 8:00 AM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello
Can you tar or zip the subject's folder and upload here.
ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
When the upload is complete, send an email to us and indicate the name
of the file.
On 3/14/19 7:27 AM, Maria-Eleni Dounavi wrote:
>
> External Email - Use Caution
>
> Dear
ht way to proceed?
>
> Thank you in advance.
>
> Best,
> Jose
>
> El mar., 12 mar. 2019 a las 17:58, Greve, Douglas N.,Ph.D.
> (mailto:dgr...@mgh.harvard.edu>>) escribió:
>
> I'm still not sure what you are trying to do. If you are
>
is working as it should.
>
> Thanks!
> Regards,
>
> On Fri, Feb 22, 2019 at 6:50 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> You can make the bonferroni correction from of mri_glmfit-sim the
> same as qdec by not including --2s
Look here, example #9
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 3/14/19 5:01 AM, Tim Hahn wrote:
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> as far as I understand, Freesurfer employs the Desikan-Killiany Atlas
> (by default) to compute the various
You can use this version of mris_apply_reg
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg
Something like
mris_apply_reg --src-xyz lh.white --lta rawavg.lta lh.white.rawavg
Where rawavg.lta is created with
tkregister2_cmdl --mov orig.mgz --targ rawavg.mgz --regheader --reg
> Hannah
> Re: [Freesurfer] Welch's t-test for HOV violation 2019-03-13 Thread
> Greve, Douglas N.,Ph.D. Hi Hannah, please include the previous
> correspondence so that we have context. Also, please remember to post
> to the list and not to us personally. thanks! doug On 3/13/19 10:
Hi Hannah, please include the previous correspondence so that we have context.
Also, please remember to post to the list and not to us personally.
thanks!
doug
On 3/13/19 10:52 PM, Hannah CK wrote:
External Email - Use Caution
Hi Dr. Greve,
Thank you for this response. Can extracting
I'm still not sure what you are trying to do. If you are running vbm,
you can usually get the T1 sampled in the MNI space for all subjects.
You can average them together and run the average through recon-all
On 3/12/19 11:44 AM, Laboratorio de Neurociencia Funcional wrote:
>
> External
Can you send the full terminal output?
On 3/12/19 10:36 AM, 310913949 wrote:
External Email - Use Caution
Hi Bruce,
I drawed a 3D ROI on the original image using freeview,and saved it as an
label file. Then I wanted to sample it to my subject and to found the closest
surface
Can you send your command line and full terminal output?
On 3/11/19 6:03 PM, Jennifer Legault wrote:
External Email - Use Caution
Hi Freesurfer experts,
I am trying to run the mris_preproc command, however I keep getting the
following error: ERROR: format for not recognized.
Even
I used to have this about 20 years ago, but I stopped supporting it when
it did not fit cleanly into the GLM ...
The shortest route is probably to do two separate analyses with
mri_glmfit, one for each group. This will output means and variances for
each group. Then use fscalc to compute maps
ence/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU
T_freeview.txt --sval-annot
yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
tkmeditfv fsaverage orig.mgz -ov
/Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
Yeo_17Net.mgz is empty.
Stefano
Il 7 mar
0.split_components.annot
tkmeditfv fsaverage orig.mgz -ov
/Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
Yeo_17Net.mgz is empty.
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D."
mailto:dgr...@mgh.harvard.edu>> ha scritto:
You have to convert the ann
When you have such a low threshold, the resulting p-values are very
liberal. See our paper https://www.ncbi.nlm.nih.gov/pubmed/29288131
Should be fine for exploratory
On 3/7/19 7:48 PM, Arsenije Subotic wrote:
> External Email - Use Caution
>
> Hello,
>
> I am planning on running a
Yea, the real hard part is figuring out how to model the twins that are split
between groups. You might be able to create a bunch of groups. If you've
already created a design in FSL that you like, you can extract the design
matrix and use it in mri_glmfit with the --X option. Not sure about
anatomical regions as well.
>
> Sparsh
>
> On Thu, Feb 21, 2019 at 12:51 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> For a volume, I would do it differently. In matlab
>
> [segcodes segnames ] = read_fscolorlut(); % read in the se
Can you include the previous emails so we have context?
On 3/7/19 6:16 PM, Sparsh Jain wrote:
>
> External Email - Use Caution
>
> Good evening.
> Thanks a lot for the help. It worked !
> While most of the labels were correct, the matlab script returned the
> wrong location for one
ctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> ------------
> *From:*
You have to convert the annotation to a volume using mri_aparc2aseg
(look at recon-all.log for an example, but note that you'll need to
specify the output so that it does not overwrite). You'll then need to
look in the output segmentation and see what the segmentation ids are
On 3/7/19 4:13
Sorry for the delay ...
This looks like a fairly complicated design, and I'm not sure how to
think about it. What do you actually want to test in the end?
BTW, the FSGD file you have there will not work. The variables are for
continuous variables (eg, age) and not discrete variables (eg, sex
ce in native space (big voxel)?
>
> On 06/03/2019 23:48, Greve, Douglas N.,Ph.D. wrote:
>> I don't think so. The surfaces are at about 1mm resolution, which should
>> be fine for this. The reason that RBV had to be upsampled is that there
>> is no way to represent the dif
Try mri_surfcluster
On 3/6/19 10:03 PM, Jahan, Bushra wrote:
> Hello,
>
> I am wondering how to generate a label in FreeSurfer from peak
> activation in a cluster - is there a specific command?
>
> Thank you.
>
> ___
> Freesurfer mailing list
>
01/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = rh
> trgsubject = fsaverage
> surfreg = sphere.reg
> ProjFrac = 0.5
> thickness = thickness
> reshape = 0
> interp = trilin
> f
Procedurally, you would create stacks (eg, mris_preproc) of the
thickness and the PET data, then you would use one as the --y input to
mri_glmfit and the other as --pvr input (in addition to your fsgd file
or design matrix). The PVR is per-voxel regresssor, so it will create a
design matrix
Your FSGD file is incorrect in several ways. Under "variables" you have
"Sex" and list "Male" and "Female". The variables must be numbers, not
strings. The variables should also represent continuous quantities, not
categories. To handle sex, you should have a total of 6 categories, the
3 that
Only one mask and one threshold is used. If you need to combine masks in
some way, you can use fscalc (or mri_binarize).
On 3/5/19 12:47 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer experts,
>
> I would like to use mri_segstats with two different masks and
>
you can use mri_segstats with the --slabel option
On 3/5/19 10:35 AM, Bruce Fischl wrote:
> Hi Kan
>
> you can give the surface-based label to mris_anatomical_stats and it
> will constrain it's calculations to the label (where it makes sense):
>
> mris_anatomical_stats -l ...
>
> you can
Can you tar up and upload the subjects to
ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
Let me know when they are there
On 3/4/19 4:59 PM, Maxime Perron wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer Experts,
>
>
> I was wondering if you have had time to look at my
What is actually in the gii file? It is expecting only to read in
overlay information (eg, a binary mask with values of 0 or 1 at each
vertex). I have not used gifti all that much
On 3/4/19 10:55 AM, CAGNA Bastien wrote:
>
> External Email - Use Caution
>
> Hi everyone,
> I need to
that mri_tessellate command should have worked. It might be a gifti
problem. Can you run it with our standard surface as an output and view
it in freeview?
On 3/3/19 11:47 AM, Max Crayen wrote:
> External Email - Use Caution
>
> Hi Bruce,
>
> we are 3D printing brains in our lab, at
Sorry Riya, you have to run it all.
doug
On 3/3/19 11:36 AM, Riya Chatterjee wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I am new to FreeSurfer - I am a high school sophomore trying to learn
> more about processing brain MRI's. I have read through most of the
> documentation,
I don't think so. The surfaces are at about 1mm resolution, which should
be fine for this. The reason that RBV had to be upsampled is that there
is no way to represent the different tissue types at a single (big) voxel
On 3/6/19 4:46 PM, Matthieu Vanhoutte wrote:
>
> External Email -
This is a bug in mris_preproc. I have created a new version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc
Copy this to $FREESURFER_HOME/bin (after making a backup of the one that
is there)
let us know if this works
On 3/2/19 8:57 AM, Chenfei YE wrote:
>
> External
look in $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt
The first number should be the one you are looking for.
On 3/6/19 12:26 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to extract stats from the hippocampal subfield volumes
>
On 3/4/19 10:11 AM, Hengameh Marzbani wrote:
>
> External Email - Use Caution
>
> Hi Freesurfers,
>
> I want to do group analysis on four groups and use the volume values
> in aseg,stats.
> 1- Is it correct that each subcortical segmentation is based on a
> "volumetric segmentation
Whitening is done by default (you can turn it off with -nowhiten to
mkanalysis-sess). It uses an AR1 model.
On 3/4/19 12:46 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Experts,
>
> May I ask if there is a whitening/weighting matrix used to give
> weighted
There was not freesurfer specific publication from dt_recon. It is
really basic, so any publication that talks about fitting tensors to the
diffusion data will do.
On 3/4/19 12:30 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> How should I go about properly
sorry, can you also include the previous emails so I know what the context is?
On 3/1/19 1:02 PM, Arsenije Subotic wrote:
External Email - Use Caution
Hi Doug,
Thank you for your reply.
My command was:
mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd CAA_CTRL_RH_Age_Sex.fsgd
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: Thursday, February 28, 2019 2:54:51 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] pr
if they are negative, it seems like a square root model is not appropriate
On 3/1/19 11:03 AM, Abhinav Yadav wrote:
External Email - Use Caution
In my case the behavioural values are already positive and negative. What about
that.
On Fri, 1 Mar 2019, 23:58 Greve, Douglas N.,Ph.D
I don't know, probably a better question for the FSL group
On 3/1/19 8:57 AM, Daniel Callow wrote:
External Email - Use Caution
Hi Doug,
I was looking at the dt_recon code and was wondering if it would be possible to
incorporate a field map into the eddy_correct portion? I tried to
have to put square root values? If yes then, how can I put negative
square roots. Since we have to put demeaned values.
Best,
Abhinav
On Fri, 1 Mar 2019, 01:44 Greve, Douglas N.,Ph.D.,
mailto:dgr...@mgh.harvard.edu>> wrote:
If you wanted to do a simple analysis looking at the effect
Did you see the line "If you seek help with this problem, make sure to
send:" and then it lists some things to send
On 2/25/19 2:13 PM, Arsenije Subotic wrote:
>
> External Email - Use Caution
>
> Dear experts,
>
> I have recently tried to use the command line to examine thickness
>
which ROIs are different?
On 2/22/19 5:39 PM, Winkelbeiner, Stephanie A wrote:
>
> External Email - Use Caution
>
> Hi Freesurfers,
>
> I’m trying to read out GM and WM values from parcels (ROIs) but get a
> different amount of ROIs for GM and WM.
>
> I use the following commands
no idea. If you want to use tbss, why not use FSL to do the dti analysis
from the start?
On 2/26/19 10:27 AM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am working through dt_recon troubleshooting (One subjects
> registration to anatomical is skewed leading
please include the previous correspondence in your emails
On 2/26/19 11:33 AM, Ella Hanns wrote:
>
> External Email - Use Caution
>
> Dear Bruce,
>
> Thanks a lot for your help!
>
> I now (roughly) ran the following pipeline but still did not manage to
> downsample my functional data in
On 2/26/19 7:58 PM, Alon Baram wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I have subject's surfaces where I first register the rh to the lh
> using xhemireg, then register both hemispheres to fsaverage_sym using
> surfreg, and then resample the registered surface to the
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