ciate your suggestions.
Thank you
John
On Mon, Nov 20, 2023 at 7:13 AM John Anderson wrote:
> Dear FreeSurfer experts, I would like to know if there is a command in
> FreeSurfer that can help me measure the distance (in voxels or mm) between
> a lesion mask and the closest voxels in the ri
External Email - Use Caution
Dear FreeSurfer experts, I would like to know if there is a command in
FreeSurfer that can help me measure the distance (in voxels or mm) between
a lesion mask and the closest voxels in the ribbon after applying recon-all
to T1 images. Thanks for your
*2Fwww.yahoo.com__;JSUl!!NZvER7FxgEiBAiR_!q-NbuKT23td_9o4DVH6jwPBlnCTPblT-heTmAHOlh6z6ucR3zZIfrZ4zbIojHZWpC28OyCiJjDFgI-IJC6-Qp_YtDOe9CqExedn8dmq0OW4$>*
+98 914 526 9298
On Saturday, October 14, 2023 at 03:29:11 PM GMT+3:3
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- FreeSurfer 5.3 QA Tools
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assuming that all preprocessing steps, fsgd file and contrasts are correct,
the choice between doss and dods could explain some of the variability
you're seeing in your results. Consider running both models and possibly
additional validation to see
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of John Anderson <
> jb19790...@gmail.com>
> Sent: Friday, September 1, 2023 12:45
> To: Freesurfer support list
> Subject: [Frees
External Email - Use Caution
Dear Freesurfer experts,
I processed DTI data using dt_recon, and I want to register FA images to
the standard MNI152 space. However, after running the command
mri_synthmorph fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz,
the registration is not
External Email - Use Caution
Let's say the red spot is overlay.nii.gz
1) convert aparc+aseg from mgz to nii.gz using:
mri_convert aparc+aseg.mgz aparc+aseg.nii.gz
2) create mask between overlay and the atlas using fslmaths:
fslmaths aparc+aseg.nii.gz -mas overlay.nii.gz
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Dear experts,
I have been using the mri_normalize in FSv7.3.2 to standardize the
intensity of FLAIR images , and I've observed that increasing the sigma
parameter up to 25 is effective in improving the quality of the normalized
images for noisy
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Dear experts,
I have been using the mri_normalize in FSv7.3.2 to standardize the
intensity of FLAIR images , and I've observed that increasing the sigma
parameter up to 25 is effective in improving the quality of the normalized
images for noisy
rect for multiple comparisons. For ROI-based
> analyses, you can use bonferroni or FDR. For maps you can use
> mri_glmfit-sim.
>
> On 4/4/2023 4:53 PM, John Anderson wrote:
>
> External Email - Use Caution
> Hello Freesurfer,
> Currently, I am using the Petsurf
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Hello Freesurfer,
Currently, I am using the Petsurfer manual, which is easily understandable
and clear. Nonetheless, I have a question regarding the "mri_glmfit" step.
As far as I know, this command is used to correct data for multiple
comparisons
with multiple volumes as expected by using the
mri_convert command with the --nslices-override argument, but I'm not sure
if I'm using it correctly.
On Mon, Mar 27, 2023 at 11:19 AM Douglas N. Greve
wrote:
> Can you try it with --dcm2niix ?
>
> On 3/25/2023 9:43 AM, John Ander
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Dear Dr Doug Greeve,
For each participant in my dataset, I have 8 mosaic volumes with 36 slices
each. I am trying to convert the DICOM files to Nifti format using the
mri_convert command in FreeSurfer version 7.3.2. However, the conversion
process
e DICOMs? It will use dcm2niix to
> convert.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *John Anderson
> *Sent:* Wednesday, March 15, 2023 1:46 PM
&
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Dear Freesurfer,
I have ASL DICOM data from a Siemens scanner in mosaic format.
For each subject, there are 64 DICOM files, which consist of both tags and
controls.
I would like to convert each individual DICOM into a separate NIfTI file or
a single 4D
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Dear Freesurfer community,
Please forgive me for the basic nature of my question.
I was wondering whether there is an argument that can be included in
mri_segstats to display the results in cubic centimeters (cm^3) instead of
cubic millimeters (mm^3).
ray_var), sqrt(csf_var)
>
> label : read hemisphere labels from and
>
> -u, -?, -help : print usage information and quit
>
> -version : print software version information and quit.
>
> On Thu, Feb 9, 2023 at 3:46 PM John Anderson wrote:
>
>> External
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You might consider the command wm-anat-snr to compute SNR
On Thu, Feb 9, 2023 at 10:38 AM Kumar, Avnish
wrote:
> You could also use these:
>
>1. For CNR you can use the mri_cnr tool:
>
> mri_cnr [options]
>
> For example:
>
> mri_cnr
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Dear Freesurfer,
I have a volumetric atlas in nifti format. I can open this atlas in
freeview. Using the Lookup Table>FreesurferColorLUT, I can see how
every label has a specific color. When I move the mouse cursor over an area
of this atlas. I can see
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Dear experts,
this is the first time I have used Freesurfer. I am a clinician and I don't
have previous experience. I followed wiki instructions. I have a group of
T1 images. I need cortical thickness and cortical gray matter volume
measurements . I
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Dear FS experts,
I would like to move PET image to MNI152. What is the correct command to do so.
I tried
mri_vol2vol --mov PET.nii.gz --s subjID --targ
$SUBJECTS_DIR/subjID/mri/orig.mga --regheader --o PET_T1.nii.gz
mni152reg --s subjID
then
this flag
represent regions of high binding affinity in patients or healthy controls or
it doesn't matter just regions known to have high binding. For example some
tracers show regions of high binding affinity on healthy scans as well as
patients scans.
On 2/22/19 11:43 AM, john Ande
.ctab. Is there any way to let
--km-ref know that I want to do whole brain normalization without feeding a
very long list of numbers?
Thank you so much for help
John
On 2/22/19 7:58 AM, john Anderson wrote:
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Hi Dr Greve,
I would like to use petsurfet t
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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) I understand that the flag
much!
John
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 Ande
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hi FS experts.
I would like to inquire about the command mri_ convert
I use this command to convert fMRI and PET 4D volumes from dicom format to
nifti.
Are there any flags that can be used in mri_convert command line to enable it
to extract a text
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Hi FS experts,
I would like to inquire about the command "dtrecon" in Freesurfer.
Is this command able to process multishell diffusion data? if not would you
recommend any method?
Thanks in advance
John___
send the full terminal output?
On 1/24/19 4:56 PM, john Anderson wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve, I appreciate your guidance very much.
>
> I followed your suggestion. I put lh.cerebellum in fsaverage and I ran
> mri_vol2surf.
> as follow
quot; even if it is the entire cerebellum as FS commands generally
require a hemisphere.
The run mri_vol2surf specifying --hemi lh --surf cerebellum
On 1/23/19 10:04 AM, john Anderson wrote:
>
> External Email - Use Caution
>
> Dear FS experts,
> I ran surface based PET analys
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Dear FS experts,
I ran surface based PET analysis on subcortical regions. Then corrected the
results for multiple comparisons using the method --grf in the command
mri_glmfit-sim.
I can visualize the output of multiple comparisons (i.e. the file
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Hi Dr Greve,
I would like to correct surface based analyses of PET data for multiple
comparisons. I ran group comparisons in three spaces. left and right
hemispheres and subcortical.
I used the method --cache in mri_glmfit-sim to correct the analyses
n specific structural surfaces such as cerebellum
and brain stem?
Thanks
John
Can you be more specific about how mri_vol2surf failed? Eg, command line,
terminal output, reason you think it did not work
On 1/21/19 10:47 AM, john Anderson wrote:
>
> External Email - Use Caut
ally correct.
>
> cheers
> Bruce
>
>
> On Tue, 22 Jan 2019, john Anderson wrote:
‐‐‐ Original Message ‐‐‐
On Tuesday, January 22, 2019 7:36 AM, john Anderson
wrote:
> Hi Dr Bruce,
> I applied your recommendations and I was able to create surfaces to the
> cerebe
commands to improve the topology of these structures?
Your guidance is appreciated,
John
Sent with ProtonMail Secure Email.
‐‐‐ Original Message ‐‐‐
On Thursday, January 10, 2019 1:37 PM, john Anderson
wrote:
> Ah! great!! thank you so much for the great help!!
> Have a good day,
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Dear FS experts,
I have a statistical map from the output of a surface based analysis in
subcortical regions. This statistical map shows significant difference between
the groups in the cerebellum cortex.
I reconstructed the cerebellar surfaces
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Dear FS experts,
I resampled PET images for multiple subjects I used mri_vol2surfe to move these
images onto fsaverage, not I have for every subject lh.PET and rh.PET
How can I create the average of multiple surfaces. For example:
on the left
aseg.mgs with fsaverage I believe. You can just
> tesselate that.
>
> cheers
> Bruce
> On Thu, 10 Jan 2019, john Anderson wrote:
>
> > External Email - Use Caution
> > Hi Dr Bruce, I highly appreciate your guidance.
> > I would like to load the cerebellum and brain
hem with mris_smooth and load them into freeview.
Shouldn't be too hard.
cheers
Bruce
On Thu, 10 Jan 2019, john Anderson
wrote:
‐‐‐ Original Message ‐‐‐
On Thursday, January 10, 2019 7:40 AM, john Anderson
wrote:
> Dear FS experts,
> For visualization purposes, is there any
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Dear FS experts,
For visualization purposes, is there any way to show the cerebellum and brain
stem regions (similar to the attached figure), this figure was published used
CONN toolbox but I am not sure how they were able to map functional data in
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Dear experts,
I have three groups:
- pre treatment (baseline)
- post treatment (follow-up after 6 month of the baseline visit)
- healthy controls.
The three groups have PET data. I ran surface based paired t test between pre
and post treatment. The
with --help to get examples
On 12/06/2018 12:31 PM, john Anderson wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve,
>> I tried to follow this web page
>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
>> This tutorial seems to be for
can I modify this command
> to fit PET data
>
> mris_preproc --target fsaverage --hemi lh \
>--meas thickness --out lh.paired-diff.thickness.mgh \
>--fsgd pairs.fsgd --paired-diff
>
> Thanks for any help!
> John
>
> ‐‐‐ Original Message ‐‐‐
> On Tues
this command to
fit PET data
mris_preproc --target fsaverage --hemi lh \
--meas thickness --out lh.paired-diff.thickness.mgh \
--fsgd pairs.fsgd --paired-diff
Thanks for any help!
John
‐‐‐ Original Message ‐‐‐
On Tuesday, November 20, 2018 6:34 PM, john Anderson
wrote:
> Dear Freesur
External Email - Use Caution
Dear Freesurfer experts,
I have multiple PET volumetric images in MNI standard space. I can average (or
get the Tmean) of these images using fslmerge then fslmaths. I would like to do
something similar on surfaces images.
I registered the images from
External Email - Use Caution
Dear Freesurfer experts,
I would like to run surface based paired t test of PET data on surface. For
every subject I have visit pre treatment and post treatment. I tried to follow
the instructions here
External Email - Use Caution
Dear Freesurfer experts,
I have the mean PET images for a number of subjects in MNI152 space. For
visualization purposes, I would like to map this mean image onto brain surface.
How can I do it. I appreciate any suggestion you may provide.
Thanks!
eight by the SNR. Still,
mathematically, this is not a true mixed effect analysis (which requires
estimates of the within and between subject noise). `
On 8/3/18 10:57 AM, John Anderson wrote:
‐‐‐ Original Message ‐‐‐
On August 5, 2018 1:04 PM, John Anderson wrote:
>> Dear FS expert
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> Dear FS experts,
> I would like to inquire about including SNR as a covariate for the between
> groups comparison in cortical thickness. Is this procedure valid? I have some
> T1 images of low quality and the majority are high in quality. I
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Daer FS experts,
I would like to inquire about including SNR as a covariate for the between
groups cpmparison in cortical thickness. Is this procedure correct
mathematically? Do I need to demean the SNA values before including it
covariates?
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Dear Dr Bruce, thank you!!
Hi John
you can try a morphological close using mri_morphology.
cheers
Bruce
‐‐‐ Original Message ‐‐‐
On August 2, 2018 3:15 PM, John Anderson wrote:
> Dear Freesurfer experts,
> I would like to i
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Dear Freesurfer experts,
I would like to inquire if there is any command/method in FS6.0 that can help
to fill holes in a brain mask without dilating it?
I would appreciate any advice!
John___
Freesurfer
External Email - Use Caution
Dear Freesurfer experts,
I would like to inquire whether there is (are) any command(s) in FS6.0 that can
help to fill holes in a brain mask without dilating it?
I would appreciate any advice,
John___
ol2surf may not be very accurate
since it uses volume-based operation.
On 7/26/18 5:19 PM, John Anderson wrote:
‐‐‐ Original Message ‐‐‐
On July 26, 2018 5:19 PM, John Anderson wrote:
> Dear Dr Greve, thank you so much. kindly have one additional question and I
> appreciate yo
Don't use --regheader, use --reg $FREESURFER_HOME/average/mni152.register.dat
On 7/26/18 4:40 PM, John Anderson wrote:
‐‐‐ Original Message ‐‐‐
On July 26, 2018 4:40 PM, John Anderson wrote:
> Dear Freesurfer experts,
> I have mask in MNI152 space. I would like to register this m
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Dear Freesurfer experts,
I have mask in MNI152 space. I would like to register this mask to fsaverage.
How can I do this registration. I am thinking of "mri_vol2surf" as follows:
mri_vol2surf --mov mask.nii --mni152reg --regheader fsaverage --o
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Dear Dr Greve, thank you for great responses and detailed explanation! Very
highly appreciated!! Thank you for sharing that valuable manuscript!
Wish you all the best,
John
On 7/25/18 8:31 AM, John Anderson wrote:
Dear Petsurfer experts,
I used
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Dear Petsurfer experts,
I used partsurfer in FS6 and had applied partial volume correction (PVC) on PET
data. I followed the same steps as in wiki which was very well explained! Thank
you!.
The analyses went fine... I would like to inquire about some
External Email - Use Caution
Dear Freesurfer experts,
I would like to inquire about the flag --subcort-gm in mri_binarize. It seems
that the final product of this flag create a mask include the brain stem which
is largely white matter. Why it was included in the subcortical gray
are looking
for, no? The space between the sulci and the ventricle volume won't directly
affect surface-based analysis, but of course the sulcal widening likely
reflects cortical atrophy that will be
cheers
Bruce
‐‐‐ Original Message ‐‐‐
On July 11, 2018 11:37 AM, John Anderson wrote
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Dear Freesurfer experts,
I have two groups of subjects (healthy and patients). The patients have
different degrees of atrophy. Looking into the individual scans, the subjects
are largely different in the space between the sulcuses and the size of
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Dear Freesurfer experts,
I ran surface based analysis between two groups using PET surfer to study the
difference in PET signal between two groups. I followed the same steps as in
wiki and everything went fine. To visualize the final statistical
--o frame1.reg.nii This
will use trilinear interpolation by default, but that is probably ok here.
‐‐‐ Original Message ‐‐‐
On July 3, 2018 2:29 PM, John Anderson wrote:
> Hi Dr Greve,
> If the individual PET frames are named: frame1.nii frame2.nii, frame3.nii ...
> fr
r that job
‐‐‐ Original Message ‐‐‐
On July 3, 2018 1:51 PM, John Anderson wrote:
> Dear Freesurfer experts,
> I have ten PET frames for every subject in my database. these frames
> represent specific time during PET acquisition. Due to head motion during
> acquisition the frames are not f
External Email - Use Caution
Dear Freesurfer experts,
I have ten PET frames for every subject in my database. these frames represent
specific time during PET acquisition. Due to head motion during acquisition the
frames are not fully overlapped on top of each other. I created
o
>
> do that is impacted by this? If you upload the subject we will take a look,
>
> but these regions are typically excluded from the surface analysis as they
>
> are non-cortical anyway.
>
> cheers
>
> Bruce
>
> On Wed, 30 May 2018, John Anderson wrot
t;
> the interior of the ?h.white surfaces. Is that what you thought was
>
> incorrect?
>
> cheers
>
> Bruce
>
> On Wed, 30 May 2018, John Anderson wrote:
>
> > External Email - Use Caution
> >
> > Dear FS experts,
> >
> > My question is ve
External Email - Use Caution
Dear FS experts,
My question is very basic and I appreciate your help.
I ran recon-all on a low quality T1 image. I'd like to fix the segmentation
error (attached).
Wm.mgz seems to be fine and the wm intensity is ~110. Can this error be fixed
by
- Original Message
On January 18, 2018 4:34 PM, John Anderson <john.ande...@protonmail.com> wrote:
It is volume-based for subcortical
On 1/12/18 8:17 AM, John Anderson wrote:
> Dear Dr Greeve,
> I interestingly read the manuscript "Different partial volume correction
Dear FS developers,
Are there any versions of "mri_coreg" that allows to output the registered
images. I mean flag "--out or -o" similar to spmregister?
Thanks for any guidance
John___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume correction
methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank
you for publishing this data.
I understood from this paper that he recommended stream for PVC is to correct
the PET images
Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume correction
methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank
you for publishing this data.
I understood from this paper that he recommended stream for PVC is to correct
the PET images
; fscalc wmparc.mask.mgz and bs.mask.mgz -o final.mask.mgz
>
> The only problem will be if the brainstem seg is higher res than wmpar
>
> On 01/10/2018 11:10 AM, John Anderson wrote:
>
>> Dear Freesurfer experts,
>
>> I want to create mask for the midbrain and the
problem will be if the brainstem seg is higher res than wmpar
On 01/10/2018 11:10 AM, John Anderson wrote:
> Dear Freesurfer experts,
> I want to create mask for the midbrain and the precentral gyrus.
> I used FSV6 to do the reconstruction. Then I used the flag
> -brainstem-structures
Dear Freesurfer experts,
I want to create mask for the midbrain and the precentral gyrus.
I used FSV6 to do the reconstruction. Then I used the flag
-brainstem-structures in recon-all to segment the brain stem.
How can I create one mask that include structures from wmpac.mgz and
Dear FS experts,
I want to extra the extra brain tissue. Is it correct to subtract orig.mgz from
aparc+aseg?
Is this provide accurate estimates forrhe space between the brain tissue and
the skull.
Kindly, do you suggest me better solution?
Thanks for any advice!
Dear Dr Bruce,
Kindly, I have question regarding the command "mri_nlfilter". I am sorry if my
questions is simple, but I highly appreciate any explanation to improve my
understanding.
I see in the man list of the command "mri_nlfilter" that it can apply Gaussian
filtering and blurring kernell.
r mris_fwhm).
On 12/12/2017 11:23 AM, John Anderson wrote:
> Dear Dr Bruce, I highly appreciate the response.
> I want to smooth PET volumetric images, when I use "fslmaths", it
> shifts the signal from the cortex to the underlying structures. I
> think (depending o
Thanks in advance!
J
> Original Message
> Subject: Re: [Freesurfer] cortical thickness smoothing
> Local Time: December 12, 2017 10:38 AM
> UTC Time: December 12, 2017 3:38 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson <john.ande...@protonmail.com
Dear Freesurfer experts,
I ran recon-all with the flag -qcache to generate smoothed cortical thickness
maps.
In order to check how the flag "-qcache" is smoothing the cortical thickness
data. I looked into the file $subj_dir/scripts/recon-all.log" which showed that
the following command was
Dear Freesurfer exerts,
I read sentences similar to this one in multiple publications (e.g.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500581/)
"Power analyses were carried out using vertex-wise variance estimates from the
coregistered cortical thickness maps, systematically varying
Dear FS experts,
I want to create mask from the atlas "aparc.DKTatlas+aseg.mgz". I need the mask
to be free of any CSF or ventricles components. Is there any way to subtract
these labels (CSF and ventricles) from the atlas "aparc.DKTatlas+aseg.mgz".
Thank you for your help
Dear FS experts,
I want to use mri_binarize to create (binarized and free of CSF and ventricles)
mask from "aparc.DKTatlas+aseg". How can I substract CSF and ventricles from
teh atlas using mri_binarize?
Thanks
John___
Freesurfer mailing list
Dear FS experts,
Is there any transformation matrix between the files /mri/orig.mgz and the file
/mri/rawavg.mgz
Please advice!
John___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
gt; UTC Time: November 30, 2017 8:54 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson <john.ande...@protonmail.com>, Freesurfer support list
> <freesurfer@nmr.mgh.harvard.edu>
>
> Hi John
>
> if your FA map is registered to the structurals (e.g. using bbregister)
Dear Freesurfer experts,
I want to register FA map in subject space to MNI. How can I do it using
freesurfer tools?
Any advice is highly appreciated!
J___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Dear Freesurfer community,
I want to visualize the mean cortical thickness map of 20 subjects. I ran the
command recon-all on the the T1 images. How can I visualize the mean cortical
thickness of one group.
Thanks for any advice
John___
Freesurfer
Dear Dr Doug,
I want to study the relationship between PET signal measured as the mean signal
of the whole cortex and gray matter volume to find regions of association
between gray matter atrophy and PET signal.
In this case I will need to run surface based analysis and the FSGD file must
be
Dear FS experts,
Are there any tools in freesurfer for 3D visualization (e.g. glass brain)? Any
recommendations are appreciated
Thanks
John___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson <john.ande...@protonmail.com>
> Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>
> you should be able to use mris_anatomical_stats I believe
>
> cheers
> Bruce
> On Wed, 13 Sep
> 2017, John Anderson wrote:
2017 6:57 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson <john.ande...@protonmail.com>, Freesurfer support list
> <freesurfer@nmr.mgh.harvard.edu>
>
> Hi John
>
> if you have run recon-all you should have a bunch of ex vivo BA labels in
> the label dir
Dear FS experts,
I have SUV maps for subjects within two groups. I moved these SUV maps into
surface then I concatenated the images in the order of two groups then I used
the compiled file in a glm analysis to check the difference between the two
groups.
I aim to use V1 Atlas to derive the SUV
Dear FS experts,
my apologizes if my question is a simple one. I am new to Freesurfer and I
appreciate if you help me.
After running recon-all on a T1 image I reached the final step and the analysis
ran smoothly without any issues.. Now what I need to check in the output images
to be sure that
---
> Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
> Local Time: August 31, 2017 4:04 PM
> UTC Time: August 31, 2017 8:04 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson <john.ande...@protonmail.com>, Freesurfer support list
> <freesurfer@nmr.mgh.harvard.edu
st 31, 2017 3:11 PM
> UTC Time: August 31, 2017 7:11 PM
> From: ebo...@mgh.harvard.edu
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, John Anderson
> <john.ande...@protonmail.com>
>
> Hi John,
>
> Which version of FreeSurfer are you running?
>
Dear experts,
looking into the output of Freesurfer in this page
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Is this
atlas can be generated with the presence of FLAIR images.
When i run recon-all without FLAIR
Dear experts,
looking into the output of Freesurfer in this page
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Do I need
FLAIR images to get this file.
I ran the command recon-all --s subj --all and I can';t find
Hi Dr Greve,
I am using pet surfer to analyze suv images. I followed all the steps in wiki,
I used the option mgx then I fed the images mgx.{ctxgm,subctxgm,gm} into
surface based analysis for left and right hemispheres. I want to inquire about
the sub cortical analysis.
1. I assume the
Hi Dr Greve,
I am using pet surfer to analyze suv images. I followed all the steps in wiki,
I used the option mgx then I fed the images mgx.{ctxgm,subctxgm,gm} into
surface based analysis for left and right hemispheres. I want to inquire about
the sub cortical analysis.
1. I assume the
> Thank you for the response
>
> It is FDG SUV map
>
> need more info, eg, what kind of map is that? what modality?
>
>> Original Message
>> Subject: mri_vol2surf
>> Local Time: August 22, 2017 11:04 AM
>> UTC Time: August 22, 2017 3:04 PM
>> From: john.ande...@protonmail.com
>>
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