Dear List Members,
Is it possible to generate tables of volume / area / thickness information
for a specific label that is not included in aparcstats or asegstats using
command line code in freesurfer (e.g. the broadman areas)? If so, could
someone point me to the instructions?
Thank you for your
@nmr.mgh.harvard.edu
Message-ID: <54aeb237.9010...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
Yep, you can use somehting like
mri_segstats --i lh.thickness --slabel subject lh lh.BA3a.label --id 1
--sum table.dat
doug
On 01/08/2015 08:50 AM, Salil Soman
Hi,
Following earlier device from this list, I was able to run the
merge_stats_tables command for a single subject as so:
merge_stats_tables --inputs $SUBJECTS_DIR/SUBJ_ID1/stats/lh.BA.stats
--all-segs --tablefile test_lh_BA_Stats_volumes.txt --meas volume
But when I tried to pass a series of su
Hi,
Is there an official thought on using freesurfer on cases were there is
volume loss after old stroke, or surgery, or trauma? I have a number of
cases were the results in general look reasonable for the remaining brain
tissue, and was was wondering if it is valid to use that data for analyses?
.
Best wishes,
Salil Soman, MD, MS
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@ k = $k + 1
> end
>
> I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I
> think there was a thread recently that suggested it might.
>
>
> On Wed, 7 Aug 2013, Salil Soman wrote:
>
> Hi,
>> I have dicoms that I turn to nifti using dc
Hi,
My understanding of etiv is that it is derived from the registration of a
brain to atlas space and not actually derived from the freesurfer
segmentation. I have a set of patients imaged at 2 time points that all
have different etiv values between the first and second scan that are
statistica
Hi,
My understanding of etiv is that it is derived from the registration of a
brain to atlas space and not actually derived from the freesurfer
segmentation. I have a set of patients imaged at 2 time points that all
have different etiv values between the first and second scan that are
statistica
r the entire series.
> It seems that you did not run your images through the longitudinal stream
> if your etiv is different across time points.
>
> For longitudinal processing see here:
> http://freesurfer.net/fswiki/LongitudinalProcessing
>
> Bes,t Martin
>
> On Nov 10,
Hi,
I hope all is well.
Was wondering if any of had heard of an explicit minimum number of DTI
directions necessary for using odf / hardi modeling ? I have run a couple
of data sets of 30 directions (+ 5 b0) through TRACULA, and have run this
same data through diffusion toolkit using the hardi /
Hi,
Is there a way to get aparcstats2table to output all of the information for
each subject, including thickness values?
Thank you,
Salil
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Hi,
Have been able to run kvlQuantifyHippocampalSubfieldSegmentations.sh to get
hippocampal subfield segmentation number of voxels. How do I convert these
values into volumes? I am guessing the voxel size of the original image is
not the correct conversion factor.
Also, I have not been able to fi
Hi,
I am writing to confirm the units for aparcstats2table for thickness and
thicknessSTD are mm, and curvature is radians. It would be a great help if
this could be confirmed.
Thank you.
Salil
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Dear Anastasia,
I am using the latest tracula code (CentOS 6 64 bit on an ubuntu 13
machine) and FS 5.3 to rerun cases I had processed with the previous
version of tracula using the new code and am getting the following errors:
*freesurfer/bin/dmri_motion: error while loading shared libraries:
l
Hi,
My cluster environment is setup to use libjpeg turbo on ubuntu 13.04 (ends
up with libjpeg.so.8.0.2 in the /usr/lib/x86_64-linux-gnu/ directory). Is
there a way to get freeview to work with a different version of libjpeg
(e.g. by making a symbolic link from libjpeg.so.62 to the libjpeg.so.8.0.
Hi,
My cluster environment is setup to use libjpeg turbo on ubuntu 13.04 (ends
up with libjpeg.so.8.0.2 in the /usr/lib/x86_64-linux-gnu/ directory). Is
it possible to use this version of libjpeg to run freeview (it currently
complaints that it cannot find libjpeg.so.62)? If so, can anyone provid
n the
diffusion tutorial do include the b0 0. Does the current version of tracula
require the b0 entries to be removed? If not, any suggestions on what I may
be doing incorrectly would be great.
Thank you.
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
F
point me to how to perform this analysis,
as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the
output files I've generated.
Thank you.
Salil Soman, MD, MS
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Thank you Martin.
I will try this approach. I was able to temporarily move the longitudinal
subject data to its own folder to run aparc2table and aseg2table. Hopefully
this will also work for the hippocampal subfield script.
Best wishes,
Sal
Salil Soman, MD, MS
Postdoctoral Research Fellow
files have non-matching number of entries. I do have the dorotbvecs option
set to 1 (as I had before). Any suggestions on what I am doing incorrectly
would be greatly appreciated. I have attached the bvec and bval files I am
providing a input.
Best wishes,
Sal
--
Salil Soman, MD, MS
Postdoctoral
-- Forwarded message --
From: "Salil Soman"
Date: Jan 12, 2014 1:28 PM
Subject: Re: problem with bvecs file with new (12/13) TRACULA code
To: "Anastasia Yendiki"
Cc:
Hi,
>
> Thank you for your email. Taking the .bval and bvec files outputed by
>
Hi,
Is there a specific issue to troubleshoot if Tracula only creates the
merged ... flt file and not the merged ... bbr file in paths? All of my
dmrirc files have both bbr and flt =1, and most of my outputs have both,
but occasionally I only get 1.
Thanks!
--
Salil Soman, MD, MS
Postdoctoral
Hi,
What is the proper way to generate a single table containing all tracula
generated statistics for all subjects in a study? I tought tractstats2table
was the way to do this, I am confused as to how trac-all -stat factors into
this process in the latest (12-09-13 version)?
Thank you.
-Sal
Hi,
I have a couple of dti cases where bbr will include forceps major and
missing forceps minor and flt will be the opposite. Similar things have
occurred for anterior thalamic tracts and cingulum bundles. Any
suggestions on what I may be doing incorrectly?
Best wishes,
Sal
___
subdirectories with path.pd.nii.gz files for
> all the tracts? Does the trac-all.log show any commands run or error
> messages for the bbr case?
>
> a.y
>
> On Sat, 18 Jan 2014, Salil Soman wrote:
>
> Hi,
>> Is there a specific issue to troubleshoot if Tracula only creates
wishes,
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
color for each isosurface as well, since the
> default is gray. You need to be in the 3D view in order to display
> isosurfaces.
> -Louis
>
>
> On Thu, 6 Feb 2014, Salil Soman wrote:
>
> Hi,
>> I generated hippocampal subfield segmentations, can generate statistics,
Hi,
I am reviewing hippocampal subfield segmentation using freeview, and was
wondering if there is a way to do multiplanar reformats so I can get
reorient the cor/sag/axial planes to that of the hippocampus?
Thank you.
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological
Hi,
Could someone point me to an example for a sample phase map that tracula
can take as input? We do not have a specific sequence for this on our GE
system but may be able to output it from some of our 3D GRE sequences.
Best wishes,
--
Salil Soman, MD, MS
Postdoctoral Research Fellow
Hi,
I was wondering what the default freesurfer coordinate space is called?
(MNI, something else)?
Thanks,
Sal
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The information in
Mar 28, 2013 at 4:22 PM, Salil Soman wrote:
> Thank you for your response.
>
> I tried re-running Tracula using bbr in a subject I had successfully run
> using flt. trac-all prep and bedp worked without an error. Bedpostx sent me
> an email confirming bedpost completed without pr
Dear Experts,
I am trying to extract FS 5.2 statistics for a single subject using the
following command:
asegstats2table --subjects SUBJECTNAME --tablefile teststats.txt
I keep getting *the following error:
*
*The stats file /PATH/SUBJECTNAME/stats/aseg.stats is not found or is too
small to be
Dear Freesurfer experts,
Could someone point me to the syntax for having recon-all use multiple T1
volumes for the same subject (which I believe it is supposed to motion
correct and average).
Thanks,
Salil Soman, MD, MS
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trix. Use mri_vol2vol and the
> registration to map the ADC map to the anatomical, then use mri_segstats to
> extract the values
> doug
>
> ps. Please post questions to the FS list instead of us directly so that
> others can benefit and it gets archived. thanks!
>
>
>
>
-- Forwarded message --
From: Salil Soman
Date: Sat, May 25, 2013 at 8:00 PM
Subject: BBR Register failing
To: Douglas N Greve
Dear Doug,
I attempted to run the process we discussed earlier today for registering a
different tissue contrast to the T1 after freesurfer 5.3 was
n Sat, May 25, 2013 at 8:23 PM, Douglas Greve wrote:
> Hi Sal, can you post this to the list instead of me directly?
> thanks!
> doug
>
>
>
> On 5/25/13 11:00 PM, Salil Soman wrote:
>
>Dear Doug,
>
> I attempted to run the process we discussed earlier toda
ments ("not" and following)
Any suggestions would be a huge help.
-Sal
On Sat, May 25, 2013 at 8:35 PM, Salil Soman wrote:
> Done. Thank you for your consideration. The best I can figure so far is
> 1) the script's attempt to make the tmp.bbregister.7392 directory fails
reve
wrote:
>
> On 5/25/13 1:39 PM, Salil Soman wrote:
>
> Thank you Doug.
>
> Just so I am clear - is the anatomical the nifti T1.mgz or is it a
> different file. From your email I gather should do the following:
>
> *1) Use bbregister to register the lowb
mri/aparc+aseg.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum
Vol_906_aparc_aseg.stats
Thanks!
-S
On Sun, May 26, 2013 at 11:11 AM, Salil Soman wrote:
> Dear Doug,
>
> Thank you for your email. Following up on our previous discussions:
>
> 1) *
As I am working with a 3D volume and not an ADC map, should I still use
--seg-erode 1 with mr segstats?
Thank
On Sun, May 26, 2013 at 1:11 PM, Salil Soman wrote:
> Hi - I realize that the --inv tag was still in my commands for mr_vol2vol
> (causing the target and the moving image
described on
http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation), I
do not find any of them.
Any suggestions on what I am doing incorrectly?
Best wishes,
Salil Soman, MD, MS
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https
make a separate call)?
recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm
-openmp 50 -hippo-subfields -all
Thank you,
Sal
On Sun, May 26, 2013 at 2:33 PM, Salil Soman wrote:
> Dear Freesurfer Experts,
>
> I have been running freesurfer 5.3 without any report
glas Greve wrote:
>
> On 5/26/13 2:11 PM, Salil Soman wrote:
>
>Dear Doug,
>
> Thank you for your email. Following up on our previous discussions:
>
> 1) *bbregister fail *- this was happening because of error from
> fslregister. The variable fsvol was translating
Dear Doug,
Thank you for your recent advise with using freesurfer to extract mean
values from non structural image data. Is there a way to generate an image
(e.g. heat map) displaying those values in free view?
Best wishes,
Sal
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03:20 PM, Salil Soman wrote:
>
>> Dear Doug,
>>
>> Thank you for your recent advise with using freesurfer to extract mean
>> values from non structural image data. Is there a way to generate an image
>> (e.g. heat map) displaying those values in free view?
>>
do this in freeview.
Any pointers to further details would be greatly appreciated.
Best wishes,
Sal
On Fri, May 31, 2013 at 12:46 PM, Douglas N Greve wrote:
> you can just specify an overlay on the freeview command line
>
>
> On 05/31/2013 03:26 PM, Salil Soman wrote:
>
>>
if you need pointers
> doug
>
>
> On 06/01/2013 04:43 PM, Salil Soman wrote:
>
>> Dear Doug,
>>
>> Thank you for your response. I am not sure I understand what I would be
>> overlaying.
>>
>> I would like to display the T1 volume for the subject, but f
Dear Doug,
Is there a way to use the Freesurfer and Tracula output to compute
connectivity maps?
Thanks!
Sal
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The information in th
Hi,
I am running freesurfer 5.3 on an ubuntu 13.04 with a nvidia card and the
the CUDA drivers installed. I am getting the following error when I try
using the use-cuda command:
Testing for CUDA device:
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVIDIA Corporation
Built on Fri_
= 768), see
attached log. Any suggestions on what I am doing incorrectly?
Best wishes,
Sal
Salil Soman, MD, MS
RZ_1484_LONG_POST.o893489
Description: Binary data
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emplate (base).
>
> Next time please send the recon-all.log file (from the subject's scripts
> directory). It gives us more information than just the screen output.
>
> Best, Martin
>
> On Jul 4, 2013, at 1:17 AM, Salil Soman wrote:
>
> Hi,
>
> I have been
Dear experts,
Could someone point me to the color key for the output of the longitudinal
analysis as viewed in freebies (as generated by the freesurfer longitudinal
analysis tutorial)?
Thank you,
Sal
Salil Soman, MD, MS
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Hi,
*Am running this command:*
$FREESURFER_HOME/bin/recon-all -i 3DSPGR.nii.gz -s WCA_248_T1Q_FS
-nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -use-cuda -all
*And am get this out put / error:*
Testing for CUDA device:
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVID
greatly appreciated.
Best wishes,
Sal
Hi Salil
what is FREESURFER_HOME set to? Is it /usr/local/freesurfer? Does
/usr/local/freesurfer/average/**RB_all_2008-03-26.gca exist?
cheers
Bruce
On Mon, 8 Jul 2013, Salil Soman wrote:
Hi,
> Am running this command:
>
> $FREESURFER_HOME/bin/
Hi,
I was wondering - is it possible to use DTI data of multiple B values in
Tracula (acquired during the same session and same TE)?
Best wishes,
Sal
Salil Soman, MD, MS
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https
helps,
> a.y
>
>
> On Sun, 21 Jul 2013, Salil Soman wrote:
>
> Hi,
>> I was wondering - is it possible to use DTI data of multiple B values in
>> Tracula (acquired during the same session and same TE)?
>>
>> Best wishes,
>>
>> Sal
>>
>>
Hi,
I have a large dataset for which I run freesurfer and confirmed that the
apar+aseg.mgz file is satisfactory. Can someone please recommend the best
way to aggregate all of the volumes/other values generated by freesurfer
into a single table for this dataset? (e.g. subjects as Rows and values by
Thank you Doug!
-S
On Sun, Aug 4, 2013 at 10:09 AM, Douglas Greve wrote:
> use asegstats2table and aparcstats2table. This will give you 3 tables
> which you could then merge into 1.
> doug
>
>
>
> On 8/4/13 12:22 PM, Salil Soman wrote:
>
>> Hi,
>>
>&
e
>
> On Sun, 4 Aug 2013, Salil Soman wrote:
>
> Hi,
>> I have a large dataset for which I run freesurfer and confirmed that the
>> apar+aseg.mgz file is satisfactory. Can someone please recommend the best
>> way to aggregate all of the volumes/other values generate
Hi,
I can run freeview using my current install on Mountain Lion, however when
I run tkmedit or tksurfer I get the following error:
GLUT: Fatal Error in tksurfer.bin: could not open display: :0.0
my /etc/profile has the setting export DISPLAY=:0.0 for a different
program. Is there settings I sh
-etiv --ctab
> $FREESURFERHOME/FreeSurferColorLUT.txt
>
> You can then run asegstats2table specifying hipposub.stats as the stats
> file
>
> doug
>
>
>
>
>
> On 8/5/13 3:39 PM, Salil Soman wrote:
>
> Dear Doug and Bruce,
>
> Thank you for your emails. I have also run the
do not see a file called mri/hippsubfieldseg.mgz for my output,
and any advice on where I could find it would be great.
Best wishes,
Sal
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Stu
sing the seg volume and the LUT
> doug
>
>
> On 08/06/2013 03:09 PM, Salil Soman wrote:
>
>
>> On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve
>> > gr...@nmr.mgh.harvard.**edu >> wrote:
>>
>> mri/hippsubfieldseg.mgz
>>
>>
>> Thank
y have the volumeStats_left.txt and volumeStats_right.txt files in the
mri subdirectory.
Again, any pointers on how to generate group stats into a table would be a
great help.
Best wishes,
Sal
On Tue, Aug 6, 2013 at 12:33 PM, Salil Soman wrote:
> Hi Doug,
>
> I realize now that I was unclear o
the script
worked and generated the 2 summary files.
Best wishes,
Sal
On Tue, Aug 6, 2013 at 12:40 PM, Salil Soman wrote:
> I can add that after running "kvlQuantifyHippocampalSubfield
> Segmentations.sh" I cannot find the nonPartialVolumeStatsLeft.txt
> and nonPartial
Hi,
I have dicoms that I turn to nifti using dcm2nii (with the default settings
plus anonymization option turned on [-a y]). The bvec files it generates by
default are 3 rows by n columns (where n is b0 number + directions). I am
under the impression tracula requires this to be converted to a n ro
while ( $k <= `head -1 bvecs|wc -w` )
> echo $x[$k] $y[$k] $z[$k]
> @ k = $k + 1
> end
>
> I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I
> think there was a thread recently that suggested it might.
>
>
> On Wed, 7 Aug 2013,
Thank you for your response. Is there a best way to review the eigenvectors
(tkmedit, freeview, other program?).
Thank you.
-S
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The
Hi,
I just wanted to confirm that label "hippocampus" in the hippocampal
subfields segmentation is simply parts of the hippocampus that do not fall
into one of the other major categories? Also, where can I find the units
for the hippocampal subfields? I am seeing some discrepancy between the
left
Hi,
When I try to run freeview on my ubuntu 13 machine, running the nvidia 5.0
cuda drivers, I get the following errors:
Xlib: extension "NV-GLX" missing on display "localhost:10.0".
Xlib: extension "NV-GLX" missing on display "localhost:10.0".
Xlib: extension "NV-GLX" missing on display "loca
and line does a window popup displaying
> spinning gears?
>
> -Zeke
>
>
>
> On 08/16/2013 05:55 AM, Salil Soman wrote:
>
>> Hi,
>>
>> When I try to run freeview on my ubuntu 13 machine, running the nvidia
>> 5.0 cuda drivers, I get the following erro
i get from dcm2nii need to have the
Y component flipped for my GE acquisitions or is this adjusted in the
tracula processing?
Thank you.
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study
Hi,
After much searching, it appears to be pretty uniform that the product DTI
sequence performed on GE requires the y gradient to be flipped. For the
datasets with which I am working diffusion toolkit, vistalab and
exploredti all require the y gradient to be flipped. However, Tracula
makes appro
growth-curves within the /transfer/outgoing/flat/greve
directory. Could someone please direct me to the correct download link for
the updated file?
Also, is there an updated version of mri_segstats for mac?
Thank you.
Salil Soman, MD, MS
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Dear List Members,
I am planning to use the eTIV for a group analysis using segmentation
volumes and I need to confirm that the eTIV ( aka ICV) generated in
freesurfer is NOT dependent on the skull strip? Specifically, I wanted to
make sure one does not need to QC the skull strips to make sure al
sed
1 slices processed
Queuing post processing stage
/mnt/glusterfs/myaccount/freesurfer/bin/bedpostx_seychelles: line 376:
14275 Terminated ${subjdir}.bedpostX/monitor
Any suggestions on what I am doing incorrectly?
Thank you,
Salil Soman, M
y would be greatly appreciated.
Best wishes,
Salil Soman
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The information in this e-mail is intended only for the person to whom it is
time to collect the
results, I find I have many more lh.hippoSfVolumes-T1.long.v10.txt (67)
than rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions on what
I may be doing incorrectly?
Thanks!
Salil Soman
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and see if that happens again.
>
> Hope this helps,
>
> best,
>
> Alan
>
>
>
> On Thu, Apr 13, 2017 at 4:49 PM, Salil Soman wrote:
>
>> Hi,
>>
>> I have run a number of cases through the FS6 hippocampal longitudinal
>> processing steps listed a
Hi,
I noticed in the output for tracula -prep I am currently running using
cvsreg it mentions openmp=1, I was wondering if there is a way to enable
more than 1 core for openmp for tracula-prep?
Thanks,
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences
dt=0.000573: new neg 23004, old_neg 23842, delta 838, rms=0.766
(0.745%)
Numerical result out of range
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veter
Hi,
I noticed that openmp is set to 1 in mri_cvs_register. However, I do not
see a way to pass on this parameter to to mri_cvs_register through dmrirc
for tracula - prep. Can anyone point me to how this can be done?
Thanks!
Sal
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time point 2. I am a little unclear on what the explanatory variable should
be performing this analysis. Any suggestions on how best to structure the
analysis would be greatly appreciated.
Best wishes,
Salil Soman, MD, MS
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When following the longitudinal qdec tutorial (
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), does
using the generate Stats Data Tables option extract data for the difference
between time point1 and 2, or something else?
Thank you.
Salil Soman, MD, MS
/surf/lh.long.thickness-rate.fwhm10.fsaverage.mgz
or .mgh file
Any suggestions on what I am doing incorrectly?
Best wishes,
Sal
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradi
Hi,
I have been following the tutorial from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial
and here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel
And I believe I am running into problems with my GLM design.
I have a set of subjects with 2 t
Hi,
Does anyone have recommendations for good automated cortical segmentation
tools for brains with infarct (so some brain missing) or tumors? I am under
the impression that FreeSurfer is not reliable in these cases. If I am
incorrect, any pointers on how to use FreeSurfer in these cases would be
Dear Doug,
Thank you again for this email. Do you think it is possible to use this
method for ASL images as well? If so, how would you change the options?
Best wishes,
Salil Soman, MD, MS
On Sat, May 25, 2013 at 11:51 AM, Douglas Greve
wrote:
>
> On 5/25/13 1:39 PM, Salil Soman
wishes,
Salil Soman, MD, MS
On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve
wrote:
> yep, you can use it for anything.
> doug
>
>
> On 9/14/14 12:52 PM, Salil Soman wrote:
>
> Dear Doug,
>
> Thank you again for this email. Do you think it is possible to use this
t overlay correctly on the T1.mgz?
> doug
>
> On 09/14/2014 11:40 PM, Salil Soman wrote:
>
>> Thank you Doug. I am having trouble with extracting statistics using
>> this method.
>>
>> I am able to use bbregister to get a transformation that registers the PD
&g
> On 09/18/2014 04:43 PM, Salil Soman wrote:
>
>> Dear Doug,
>>
>> Thank you for your email.
>>
>> The registration overlap looks reasonable. Thank you for considering this
>> question.
>>
>> Best wishes,
>>
>> Sal
>>
>>
Dear Doug,
Thank you for your email.
On Wed, Sep 24, 2014 at 8:57 AM, Douglas N Greve
wrote:
>
>
>> 2) While most of the CBF to T1 registrations using the transformation for
>> the PD to the T1 image worked reasonably, there are a few where the
>> registration is a little off (almost exclusivel
Dear List Members,
Does anyone know if it is possible to use freesurfer gpu based acceleration
using amd video cards?
Thanks,
Salil Soman, MD, MS
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be properly formed, as I can read it directly
into freesurfer and get a properly formed image. Was wondering if anyone had any
suggestions as to what may be going wrong?
Thanks,
Salil Soman
[EMAIL PROTECTED]
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Freesurfer
ed by mri_convert from spm files.
Thanks,
Salil Soman
[EMAIL PROTECTED]
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are applied to the images by the .reg file) The end result I'm
looking for is that is both images are loaded into freesurfer with a reg file
that applies no transforms, the images will be the same as though the original
.reg file was used.
Thanks,
Salil Soman
[EMAIL PROT
transforms are applied to the images by the .reg file) The end result I'm
looking for is that is both images are loaded into freesurfer with a reg file
that applies no transforms, the images will be the same as though the original
.reg file was used.
Thanks,
Salil Soman
[EMAIL PROT
External Email - Use Caution
Hi,
I am passing synthstrip an nii.gz file, and it keeps giving the error
"ValueError: cannot determine file format from extension for test " (full
error below). Any suggestions on how to fix this issue? The nifti files was
made from dicom images usi
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