hite matter atrophy
Local Time: April 20, 2017 10:04 AM
UTC Time: April 20, 2017 2:04 PM
From: ayend...@mgh.harvard.edu
To: John Anderson , Freesurfer support list
Hi John - Unless someone else has a better idea, the aseg (subcortical
segmentation) contains left and right cerebral and cerebellar whit
Dear FS experts,
I want to inquire if there are any threshold for the flag "gcut " in the
command:
recon-all -skullstrip -clean-bm -gcut -subjid
If this not available are there any tools that can help to control how much
dura will be cut out
Thanks in advance!
John
Hi Doug,
Thank you for the detailed explanation!
Please I have one follow-up question and I highly appreciate your input
How can we explain results related to reduce cortical thickness and normal gray
matter volume. Are these parameters two different thing or they are related to
each other.? In o
volumetric measures ?
Thank you for any advice!
You are speaking statistically, I assume? Ie, you see a sig change in volume
and not thickness, or vice versa? If so, it can easily be explained by
differences in noise
On 5/2/17 5:00 AM, John Anderson wrote:
Original Message
Subject
By noise, I just mean variability, which could come from those sources, but
more likely come from intersubject variability. No good way to check those. It
is looking like volume analysis has much higher false positive rates than
thickness too.
On 5/2/17 12:29 PM, John Anderson wrote:
--
Dear Doug,
I have Bold fMRI data (6 minutes of acquisition which is equal to 180 volume
for every run). The total number for images is 140 (50 controls and 90
patients). I plan to use FSFAST (FS V6.0) to study:
1. The difference between the groups in global functional connectivity
2. Seed-based f
Dear Freesurfer experts,
I know that the grey or white matter volume measures for the ROIs reported in
"wmparc.mgz" can be adjusted for the total intracranial volume Is is
correct to do the same for surfaces? I mean can the surface of an ROI (e.g.
precentral) be adjusted to total surface are
. But adjusting by
total surface area is ok too.
On 05/08/2017 02:29 PM, John Anderson wrote:
> Dear Freesurfer experts,
> I know that the grey or white matter volume measures for the ROIs
> reported in "wmparc.mgz" can be adjusted for the total intracranial
> volume I
Dear Dr Doug,
I have two groups of subjects (80 patients and 40 controls). I analyzed the
data using Freesurfer v6.0.
I want to study the difference between the groups in "precentral gyrus volume".
After "recon-all" I built Qdec table and I used Qdec to compute the comparison
by including eTIV a
folded surface,
the surface area actually goes up linearly with the volume. But adjusting by
total surface area is ok too.
On 05/08/2017 02:29 PM, John Anderson wrote:
> Dear Freesurfer experts,
> I know that the grey or white matter volume measures for the ROIs
> reported in "w
can be used to test ROI volume.
On 05/09/2017 05:58 PM, John Anderson wrote:
> Dear Dr Doug,
> I have two groups of subjects (80 patients and 40 controls). I
> analyzed the data using Freesurfer v6.0.
> I want to study the difference between the groups in "precentral gyrus
&
Dear Freessurfer experts,
i want to convert IMA files to nifti using mri_convert I did the following:
mri_convert 54365413.ima output.nii
I got this error
WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
... continuing.
if I run mri_info on output.nii I see
voxel-to-ras dete
Hi Doug thank you for the quick response!
The source is a Siemens scanner. Data derived from the Spine. I don't know what
is the optimal way to convert these ima images to nifti
what is the source of the ima file? was it anonymized? You can try something
like adding
-iid -1 0 0 -ijd 0 1 0 -ikd
Dear experts,
i want to know if the eTIV can be used to adjust non-morphometric measures like
,diffusion, PET, ASL ,, etc.
Can these measures be adjusted to eTIV. if yes what is the correct command to
be used?
Thank you
Jon___
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Dear TRACULA experts,
I plan to use TRACULA in freesurfer 6 to analyze DTI data. I want to kindly to
inquire about the command "dmri_motion".
This script,nicely, generates: the SNR, drop out score, # drop out slices and
motion parameters.
I highly appreciate if you can guide me to a method, so I
Dear Freesurfer experts,
I have T1 and T2 images were unfortunately acquired with different resolution (i.e the voxel sizes is not the same)
T1 is 280X280X208
T2 is 270X270X200
I tried to run "recon-all" but it failed to process the data. The command that I used is :
pbsubmit -c " recon-all
/002.mgz.
Jon
Sent: Sunday, June 11, 2017 at 2:12 PM
From: "Matt Glasser"
To: "Freesurfer support list"
Subject: Re: [Freesurfer] difference in T1 and T2 resolution
What was the error message?
Peace,
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard
Thank you for your response. The log file is attached
Sent: Tuesday, June 13, 2017 at 2:02 AM
From: "Douglas Greve"
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] difference in T1 and T2 resolution
can you send the log file?
On 6/11/17 10:08 PM, John Ande
s probably not a good idea to try to combine them, but if you really want to, I can supply you with a solution.
On 6/14/17 1:12 PM, John Anderson wrote:
Thank you for your response. The log file is attached
Sent: Tuesday, June 13, 2017 at 2:02 AM
From: "Douglas Greve&q
Dear experts,
I have image and mask and I want to subtract the mask from the image. Meaning I want to get image free of specific anatomical region. For example,
I have image T1.nii for the brain and mask for the thalamus. How can I remove the thalamus from the T1 image to get T1 image free of th
the brain. I highly aprreciate any suggestion.
Sent: Thursday, June 15, 2017 at 1:19 PM
From: "Bruce Fischl"
To: "Freesurfer support list"
Subject: Re: [Freesurfer] substract images
Hi Jon
mri_mask should do the trick
cheers
Bruce
On Thu, 15 Jun 2017, John Anderson wr
t"
Subject: Re: [Freesurfer] substract images
Hi Jon
use mri_binarize on your initial mask to create a new one for mri_mask (use
--min and --max to specify the input mask intensity ranges that you want to
be "on"), then give that to mri_mask
cheers
Bruce
On Thu, 15 Jun 2017, John Anderso
al 1
mri_mask T1.nii mask.rev.nii T1.masked.nii
cheers
Bruce
On Thu, 15 Jun 2017, John Anderson wrote:
> Hi Bruce, the mask is already binariz (min=0 ; max=1)
> I tried
> mri_mask T1.nii mask.nii output.nii
>
> The output is a maked image meaning the structure behind the mask
Dear Freesurfer experts,
I have T1 images acquired using CT scan not MRI. I have the following questions
please:
1. "mri_convert" failed to convert the dicoms to nifti, so I used "dcm2nii"
part of mricron to convert the dicoms to nifti. I am wondering if there are any
tools in Freesurfer to conv
Dear Freesurfer,
Are there any tools in Freesurfer that can help to convert PET DICOMs to nifti
files?
Thank you for your help and for any suggestion
Jon___
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17 9:12 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson , Freesurfer support list
>
> Hi Jon
> have you tried mri_convert?
> cheers
> Bruce
> On Wed, 19 Jul 2017, John Anderson wrote:
>> Dear Freesurfer,
>> Are there any tools in Freesurfer that can help to conv
Dear Dr Greeve,
I am new to FSFAST so I highly appreciate your response.
I have resting state fMRI data and I am following the steps as reported in wiki.
My questions is regarding motion evaluation. The attached figure is an output
of "plot-twf-sess".
1. Given the plotted data can we say that incl
Dear Dr Greve,
I am new to FSFAST so I highly appreciate your response.
I have resting state fMRI data and I am following the steps as reported in
wiki. I want to study the difference in functional connectivity between two
groups
My questions are regarding motion evaluation and the contrasts.
1.
-sess, you include this as the contrast. See the
wiki for more details
On 8/2/17 12:34 PM, John Anderson wrote:
Dear Dr Greve,
I am new to FSFAST so I highly appreciate your response.
I have resting state fMRI data and I am following the steps as reported in
wiki. I want to study the differen
FastFunctionalConnectivityWalkthrough
>
> When you make your analysis, you need to include something like -taskreg
> L_Posteriorcingulate.dat
>
> Then when you run isxconcat-sess, you include this as the contrast. See the
> wiki for more details
>
> On 8/2/17 12:34 PM, J
t; http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
>>
>> When you make your analysis, you need to include something like -taskreg
>> L_Posteriorcingulate.dat
>>
>> Then when you run isxconcat-sess, you include this as the contrast. See the
gt; UTC Time: August 7, 2017 5:54 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson , Freesurfer support list
>
> Hi John
> I think the FSL group has some nice tools to fix these distortions either
> with or without field maps (topup for example)
> cheers
> Bruce
&
Hi Dr Greve,
I have PET data for two groups and I used PET surfer in FSV 6.0 to run the
analyses. The pipeline is straightforward and the analysis ran smoothly without
any issues.
Is it correct procedure to adjust PET signal to differences in gray matter
volume or cortical thinness between two
wiki.
On 08/10/2017 04:11 AM, John Anderson wrote:
>
> Hi Dr Greve,
>
> I have PET data for two groups and I used PET surfer in FSV 6.0 to run
> the analyses. The pipeline is straightforward and the analysis ran
> smoothly without any issues.
>
> Is it correct proced
o the analysis images in the
native space then we re sample the images to the brain surface that's why we
apply PVE? Is the registration to standard template exacerbates PVE?
On 08/10/2017 11:35 AM, John Anderson wrote:
>
> Dear Dr Greve,
>
> Thank you very much for the gre
Dear Freesurfer experts,
I have noisy four MEMPRAGE images each one has four volumes for the same
participant. These T1 images were acquired at the same scanning session. I have
two question:
1. Is there any tool in free surfer to average these images.
2. Is the average the images a good idea to
> Subject: Re: [Freesurfer] T1 motion and average
> Local Time: August 15, 2017 6:04 PM
> UTC Time: August 15, 2017 10:04 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson , Freesurfer support list
>
>
> Hi John
>
> sure, mri_average -rms will take
Hi FS experts,
Is there any way to convert the registration matrix reg.dat to reg.lta?
Thank you
John___
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The information in this e-mail
ocal Time: August 17, 2017 1:54 PM
> UTC Time: August 17, 2017 5:54 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson , Freesurfer support list
>
>
> I think lta_convert will do the trick. Check out the help
>
> cheers
> Bruce
> On Thu, 17 Aug
> 2017, John
Hi Dr Greve,
I followed the steps in WIKI to do SUV-surface based analyses + PVC. I have the
following questions and I highly appreciate your input:
1. Why the dimension of the images (mgx.gm, mgx.ctx.gm and mgx.ctx.subgm) is
not like the original SUV image that has been fed to the pipeline. i.
AM, John Anderson wrote:
Hi Dr Greve,
I followed the steps in WIKI to do SUV-surface based analyses + PVC. I have the
following questions and I highly appreciate your input:
1. Why the dimension of the images (mgx.gm, mgx.ctx.gm and mgx.ctx.subgm) is
not like the original SUV image that has
Dear Dr Greve,
Kindly, I wanted to know why "mri_coreg" apples smoothing during registration.
e.g.
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
Are there any effects on the accuracy of smoothing if I turn off this default
feature (specifically in pet surfer pipeline).
mri
gt; analysis so I am curious about this difference between the images.
>
> Thanks for any clarification!
>
> On 8/18/17 10:20 AM, John Anderson wrote:
>
> Hi Dr Greve,
>
> I followed the steps in WIKI to do SUV-surface based analyses + PVC. I have
> the following questions an
12:15 PM, John Anderson wrote:
>
> Dear Dr Greve,
>
> Thank you so much for the detailed explanation. I have additional
> question and I highly appreciate any clarification.
> By reviewing the log file "mri_gtmpvc.log" I see that this program
> apply smoothing F
reference that
mri_gtmpvc rely on it to measure it?
Thank you for any clarification!
John
read the petsurfer page for how to select the psf
On 08/21/2017 04:52 PM, John Anderson wrote:
\
> Original Message
> Subject: Re: smoothing
> Local Time: August 21, 2017
Dear FS experts,
I ran voxel-wise analysis between two groups using randomise in FSL and the
final statistical maps is as attached.
I aim to to repeat the analysis using surface based analysis. I followed the
steps as in wiki. I am not sure what is the correct value for projfrac int he
command
> 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
>> T
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 analysi
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 analysi
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
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 o
August 31, 2017 3:11 PM
> UTC Time: August 31, 2017 7:11 PM
> From: ebo...@mgh.harvard.edu
> To: Freesurfer support list , John Anderson
>
>
> Hi John,
>
> Which version of FreeSurfer are you running?
>
> Emma
>
> -
>
> Emma Boyd
>
> Research
> 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 , Freesurfer support list
>
> "Boyd, Emma"
>
> Hi John
>
> the atl
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 t
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
2017 6:57 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson , Freesurfer support list
>
>
> Hi John
>
> if you have run recon-all you should have a bunch of ex vivo BA labels in
> the label dir.
>
> cheers
> Bruce
> On Wed, 13 Sep 2017, John Anderson wro
11 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson
> Freesurfer support list
>
> you should be able to use mris_anatomical_stats I believe
>
> cheers
> Bruce
> On Wed, 13 Sep
> 2017, John Anderson wrote:
>
>> Thank you Dr Bruce,
>> The stat values for ever
Dear FS experts,
Are there any tools in freesurfer for 3D visualization (e.g. glass brain)? Any
recommendations are appreciated
Thanks
John___
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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 "O
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 mail
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___
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PM
> UTC Time: November 30, 2017 8:54 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson , Freesurfer support list
>
>
> Hi John
>
> if your FA map is registered to the structurals (e.g. using bbregister)
> then you would just compose that transform with the talairach.
Dear FS experts,
Is there any transformation matrix between the files /mri/orig.mgz and the file
/mri/rawavg.mgz
Please advice!
John___
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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
Freesurfe
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
John__
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 processing
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 appl
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 , Freesurfer support list
>
>
urf or 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
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.
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!
J_
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
brainstemSsLabels
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 precentral gyrus.
> I used FSV6 to do the reconstruction. Then I used the flag
> -brainstem-struct
ask.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 precentral gyrus.
>
>> I used
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 using
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 using
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___
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-- Original Message
On January 18, 2018 4:34 PM, John Anderson 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
> methods lead to different conclu
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 sett
> 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
you want to
>
> 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 And
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 tem
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
--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 ...
> frame10
External Email - Use Caution
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 maps,
External Email - Use Caution
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
ven
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
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
External Email - Use Caution
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 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
External Email - Use Caution
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
mask_
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 t
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 your
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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___
Freesur
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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 mai
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Dear Dr Bruce, thank you!!
Hi John
you can try a morphological close using mri_morphology.
cheers
Bruce
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On August 2, 2018 3:15 PM, John Anderson wrote:
> Dear Freesurfer experts,
> I would like to inqu
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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? Finally,
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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 reviewed
you weight 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:
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On August 5, 2018 1:04 PM, John Anderson wrote:
>> Dear FS e
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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!
Joh
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