Look in $FREESURFER/FreeSurferLUT.txt
This has those indices (and a lot more). If you want just the hippo SF
indices, you can run something like
mri_segstats --seg hipposf.mgz --ctab-default --sum sum.dat
The indices will be in sum.dat
On 5/14/2024 11:04 AM, karl landheer wrote:
The first one will test for a difference between group offset/intercept
accounting for age, gender, episodes, and residuals. By setting a
regressor contrast element to 0, one accounts for that variable because
the variable appears in the model that is fit to the data (and so its
effects
are doing well. Yesterday, I had some questions regarding
normalization in Freesurfer. Thanks to Dr. Douglas N. Greve, I
received answers for all of them. However, I still have one more
question.
When I normalize brain surfaces to eTIV, they appear to be in two
different units (mm2 and mm3
They are not identical, for sure. In general, I discourage people from
modeling categorical variables (eg, Group1/2 below) as continuous
variables because you make assumptions that might not be reasonable (eg,
females will have twice the thickness as males). I would use the first
method.
On
not sure what you mean and/or referring to. can you elaborate?
On 5/7/2024 4:03 PM, L wrote:
External Email - Use Caution
Dear exports,
I am wondering whether the outcomes of the longitudinal two stage
model is tp1 - tp2 or tp2 - tp1.
Thank you,
Lihong Wang
--
- Lihong
Sincerely,
Yilei
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, April 18, 2024 2:57 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] recon-all process still not fin
On 5/2/2024 4:03 AM, yunus soleymani wrote:
External Email - Use Caution
Hello freesurfers,
I have some questions about the output variables of Freesurfer:
1. In the case of brain volume normalization, do I need to normalize
all the volumetric results to the eTIV or just the
I would use either the ocn (cluster annotation) or the cluster-wise
corrected map: overlay as you generally don't want to show uncorrected
data. As for the max, it is a personal choice, just what you think looks
good or makes your point.
On 4/22/2024 7:52 AM, Asuka Toyofuku wrote:
bbregister is more sensitive to the smoothing in the PET images. This
can create a confound between atrophy and registration. bbregister
should only be used on non-smoothed data.
On 5/1/2024 5:06 AM, Ruben Dörfel wrote:
External Email - Use Caution
Hi FreeSurfer Team,
I am
not sure what is happening. You can run recon-all with -debug and
capture the output (both stdout and stderr) into a file. This will cause
it to print out huge amounts of text specifying what it is doing on each
line. You should also see if there is some stderr output that is not
being caught.
Sorry, I don't know what you mean by enorm threshold. Can you elaborate?
On 4/4/2024 4:39 PM, Sneha Pandya wrote:
External Email - Use Caution
Dear team,
I am using mc-afni2 to perform motion correction on dynamic PET images
(ref: petsurfer wiki page). I am planning to use an
On 4/18/2024 1:59 PM, Tejaswi D. Sudhakar wrote:
External Email - Use Caution
Hello Freesurfer team,
I am interested in doing one glm analysis using both the thickness and
cortical surface area.
My question is two-fold:
First, is it possible to provide both the thickness and
thanks, just checked in your change.
On 4/17/2024 9:37 PM, Tyler Slouf wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I found what I believe to be a bug. Typically I can load mgz files
into my Matlab program without any trouble.
But if the path containing the mgz
You can try running samseg. This will generate most of the layers you
want, but in segmentations. You will have to convert them to surfaces
(eg, mri_tesssellate or mri_binarize with --surf output)
On 4/15/2024 5:31 AM, XIE Jing wrote:
External Email - Use Caution
Hello all,
We
Yes, you can also run
mris_fwhm --smooth-only --i input.surf-values.mgz --fwhm FWHM --s
subject --hemi hemi --o output.surf-values-smoothed.mgz --cortex
This will give the same result as mri_surf2surf
On 4/12/2024 10:07 PM, Jiaen Liu wrote:
External Email - Use Caution
I found in
The vsm (voxel shift map) needs to be in the same voxel space as the
fMRI (ie, it has to have the same voxel size, number of voxels, and the
voxels must line up with the fMRI)
On 4/11/2024 8:11 PM, Gianluca Guglietti wrote:
External Email - Use Caution
Hi,
I had a question as to
vertices require a surface. There is no surface for cerebellum, so the
vertices are all marked -1 to indicate that the vertex indices are not
valid. The XYZ values are valid though
On 4/9/2024 6:36 AM, Sam W wrote:
External Email - Use Caution
Hello!
I'm trying to convert the
No, not any more. We used to have it, but it was too hard to maintain.
You can always run in parallel on the CPU (-threads N)
On 4/3/2024 2:58 PM, Camargo, Aldo wrote:
External Email - Use Caution
Hi there,
I was wondering if there is support for GPU on FreeSurfer. I really
would
You have a space in your current path (between severe and similar). That
is causing the problem
On 4/1/2024 8:26 AM, Huang, Yujing wrote:
There is a space in your path
‘/home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe
similar/first_sT1W_3D_TFE_tra_MR350895.nii’.
Rename the directory
Done
On 3/29/2024 3:31 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
I am currently running FreeSurfer 7.4. I wrote a script using the
program mri_volsynth. I noticed for the first time the program was
trying to write files where it did not have write permissions. It
what do you mean "extract" the cluster? Do you want mean thickness for
each cluster? Or the mean contrast? Of all the voxels in a cluster? For
the first two, you can use something like
mri_segstats --seg clusterseg.mgz --i contrast.mgz --sum summary.txt
On 3/26/2024 9:47 AM, Liliana Wu wrote:
What are the errors that you are facing? Can you provide more detail?
On 3/26/2024 9:12 AM, Saifullah Tumrani wrote:
External Email - Use Caution
I am using freesurfer to preprocess my t1w 3d Mris using autorecon1
which includes first 5 preprocessing techniques till skullstripping it
Is that an MP2RAGE? The background may be messing things up. You can try
masking it, eg,
mri_synthstrip --i yourimage.mgz --o stripped.mgz
Then pass stripped.mgz to recon-all
On 3/25/2024 6:33 AM, Chen Yang wrote:
> External Email - Use Caution
>
> Dear FreeSurfer Developers,
>
> I am
-
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, March 21, 2024 9:44 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied
to PET data with single frame?
Yes, though that will n
oops, should have read your 2nd email. Yes, jacobian is the reason
On 3/20/2024 5:34 AM, tyzh...@ibp.ac.cn wrote:
External Email - Use Caution
Dear FreeSurfer Experts,
Sorry, I think I've found the answer. It's because Jacobian correction
was performed for mris_preproc, right?
When working with area, you need to turn on jacobian correction.
mris_preproc will do this automatically, but you have to add --jac to
mri_surf2surf explicitly
On 3/20/2024 4:31 AM, tyzh...@ibp.ac.cn wrote:
External Email - Use Caution
Dear FreeSurfer Experts,
I'm currently working
the -expert
options file that you suggested anyway, but it exited with errors
unfortunately and didn’t work. Is there anything else we can try?
Thanks again for your help!
Best,
Maria
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Date: *Wednesday, March 6
urfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Wednesday, March 20, 2024 11:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied
to PET data with single frame?
you cannot apply kinetic modeling to one frame. W
See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
On 3/18/2024 4:38 PM, Vivek Kandasamy wrote:
External Email - Use Caution
Hello,
So I ran FreeSurfer to get numeric data from MRI images and got these
files under the stats page.
Screenshot 2024-03-18
occurs on:
fcseed-sess -s ID -cfg wm.config -overwrite
ERROR: could not determine file for rs-fMRI_AROMA/ID/rest/001/fmcpr
Best regards
Stefano
Il giorno 19 mar 2024, alle ore 15:54, Douglas N. Greve
ha scritto:
Hi Stefano, I think I found and fixed the problem. Can you try these?
On 3/19/2024
you cannot apply kinetic modeling to one frame. What is you ligand? For
a one frame acquisition, you usually use an SUV analysis.
On 3/20/2024 12:03 AM, WONG Wan Wa wrote:
External Email - Use Caution
Hi experts,
As stated in the subject, can kinetic modeling be applied to PET data
very much!
Stefano
Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi
ha scritto:
Thank you.
I’m attaching the file.
Stefano
Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve
ha scritto:
can you send me this file
/Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess
On 3
I've looked into this a little bit.
I looked at the area of the original manual labels for entorhinal as
found in the aparc. They do show a lh>rh asym of 3%, but it is not
significant (p=.45).
I looked at the automatic labels in two other large data sets. I found
significant lh>rh asym of ento
It is not really something that can be converted to an overlay (gifti or
otherwise). It is a probabalistic atlas with prior probabilities for
each label as well as curvature mean and stddev for each label at each
point in space. If you know some C++, you can look at GCSAread() in
gcsa.cpp to
!
Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve
ha scritto:
entire terminal output
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail
Hi Bram, try using mris_surfseg2vol. Look in the recon-all log file for
an example usage
doug
On 3/10/2024 12:43 PM, Bram Diamond wrote:
External Email - Use Caution
Hello FreeSurfer Experts!
I’m having trouble projecting the Yeo 17n annotation to volume space.
I’ve tried on FS
And how does the parcellation look on the surface?
On 3/7/2024 9:53 AM, Hyunchul Lee wrote:
External Email - Use Caution
Yes, it looks fine to me
Those dots seem to lie on the pial surface
On Thu, Mar 7, 2024, 10:07 PM Douglas N. Greve
wrote:
Have you looked at the actual
Have you looked at the actual surface?
On 3/7/2024 2:29 AM, Hyunchul Lee wrote:
External Email - Use Caution
Hello,
I'm using Freesurfer recon-all to create reconstructions to use with
MNE-python for source estimation of SEEG data. My work relies on
having correct labeling of
Yujing, you can just send Taylor a binary that can be put in the local
version of $FREESURFER/bin
On 3/6/2024 11:45 AM, Huang, Yujing wrote:
Hi Taylor,
Thanks for sharing the data.
I see the problem now. The first 14336 bytes of your rh.area fit
SIGNA_FILE criteria. So, it is read as
hL5PxfcxxZg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3767398%2F>
and it mentions biases when doing registration of a hemisphere to
either LH or RH but I am not sure if these are the same biases.
Thanks!
-joost
On Wed, Nov 29, 2023 at 12:02 AM Douglas N. Greve
wrote:
Yes,
No, sorry. We do have FS containers that you could use on AWS
On 3/6/2024 9:28 AM, Gonzalo Rojas Costa wrote:
External Email - Use Caution
Hi:
Is there a freesurfer facility where an MRI study can be processed
remotely?
Sincerely,
Gonzalo Rojas Costa
Can you be more specific about what abnormality you are seeing? The
Screenshot2 does not look so bad to me. I'm assuming that this is the
talairach.xfm transform you are talking about? If so, that is hardly
used in the stream (and certainly not for placing surfaces), so it is no
surprise that
resolve our issue enough to make the image usable for our analyses, so
I wanted to see if there was anything else we could do to resolve the
problem.
Thank you!
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Date: *Tuesday, March 5, 2024 at 9:11 AM
The easiest thing is to set up contrasts to pull out the parameters you
want. The next easiest (or maybe the easiest) is to look in the beta
file. It will have a frame for each column in the design matrix. The
value is the regression coefficient.
On 3/5/2024 11:33 AM, Hoskinson, Kristen
Most of the info has been lost for that scan. It was a GE 1.5T scanner;
subject is a male, approx 37yo
On 3/4/2024 2:49 PM, Shounak Nandi wrote:
External Email - Use Caution
Hi,
I have used the *bert
.| **Graduate Student*
Medical/Clinical Psychology Doctoral Program
UAB |/The University of Alabama at Birmingham/
mstan...@uab.edu <mailto:mstan...@uab.edu>
Pronouns: she/her/hers
Image
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Date: *Sunday, M
Can you send pictures of the slices showing the problem?
On 3/3/2024 3:18 PM, Stanica, Maria wrote:
External Email - Use Caution
Hello FS developers,
I ran my subjects through skullstripping and recon-all. Everything
processed correctly (and exited without errors), except 4 images
Can you include an image with and without the surfaces? Make sure to
include slices where you think the white surface extends too far.
On 2/28/2024 9:13 AM, Luisa Klahn wrote:
External Email - Use Caution
Dear Douglas,
Please find the nu.mgz screenshot attached.
Best,
Luisa
Yes, you can use the siemens STC option (ie, -stc siemens)
On 2/26/2024 9:02 PM, Maria Hakonen wrote:
External Email - Use Caution
Dear all,
Have I understood correctly that the slice delay of each slice is not
needed when performing slice time correction with preprocess-sess?
I
think it is FrreSurfer default method to segementation.
Lejia
At 2024-02-27 01:24:00, "Douglas N. Greve" wrote:
what did you use the do the segmentation? Include command line and
terminal output
On 2/26/2024 10:46 AM, lejia2011411409 wrote:
External E
Lab
Helen Wills Neuroscience Institute
University of California, Berkeley
On Fri, Feb 23, 2024 at 10:26 AM Douglas N. Greve
wrote:
Can you send more info? Eg, command line, all terminal output,
version of FS you are using?
On 2/6/2024 6:18 PM, Michael Ruvalcaba wrote
what did you use the do the segmentation? Include command line and
terminal output
On 2/26/2024 10:46 AM, lejia2011411409 wrote:
External Email - Use Caution
Dear freesurfer experts,
A large amount of subjects got segmentation white matter bad (some
dark white matter cannot be
unning at a certain point.
What do you think?
Best regards,
Asuka
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* 23 February 2024 19:30
*To:* freesurfer@nmr.mgh.harvard.edu
*Subjec
It looks like the volume has very poor contrast. What volume are you
displaying it on? Can you take a pic on the nu.mgz?
On 2/26/2024 2:53 AM, Luisa Klahn wrote:
External Email - Use Caution
Dear Douglas,
Please find attached the pictures for the following issue:
I am processing
F8XZrhB_Rknetjx1FVS8u1BBOZ16mMYnGswaNPzNgbt15-7OR0ZajBrz3jJMaAXx2tGeFbJuIT_cwpTPX2u7uVcKu40byzK3CksUD9sBXUODMzo1dWFYJ7dqv9jzjPyhXiM51d49k7iGamx_SlWvcrdjka0R328JXdXbqwiXqt2FEwAVsz1ioBdFbSPNdth73sqgmm1hDt5vQsBMMp8Txr8bGJeZxE6q-ZHf8yqwxiFsXOOVtBw/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC9724189%2F>).
On Fri, Feb 23, 2024 at 10:27 AM Douglas N. Greve
wrote:
Sorry, don't
N. Greve
*Sent:* Friday, February 23, 2024 11:03 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] consistency in recon-all parallel pipeline
So, is the bottom line that when you run 7.4.1 on COS8 in parallel
that you get (slightly) different results each time?
On 2/2/2024 11
you can run recon-all on the mni152 to get the aparc+aseg.mgz, then take
the temporal lobe from that
On 2/23/2024 11:29 AM, Camargo, Aldo wrote:
External Email - Use Caution
Hi there,
I would like to know where I can find a mask in MNI space for the
temporal lobe.
Thanks a lot in
Just sample the activation onto the full surface (eg, --surf white
--projfrac 0.5), then just load it as an overlay when you view the patch
in freeview
On 2/22/2024 12:18 PM, Atena Akbari wrote:
External Email - Use Caution
Hello Freesurfer team,
I have flattened the occipital
You can run mri_vol2surf to sample the ROI onto the surface, eg,
mri_vol2surf --regheader subject --mov yourROI.mgz --projfrac-max 0 1 .1
--hemi lh --o lh.yourROI.mgz
yourROI.mgz should be voxel-for-voxel aligned with the orig.mgz
View your sample with
tksurferfv subject lh inflated -aparc -ov
Can you include the full terminal output for one of the mris_preproc
commands that is failing?
On 2/22/2024 7:12 AM, Asuka Toyofuku wrote:
External Email - Use Caution
Dear Freesurfer experts,
I have issues with creating a custom registration template. (I'm
following this
Do you see a subject/stats/lh.w-g.pct.stats file?
You can use asegstats2table to compile this across subjects. Run it with
-help to get more info
On 2/22/2024 3:26 AM, ERNEST KISSI wrote:
External Email - Use Caution
I processed several items of data. And I have rh.w-g.pct file in
Yes, you just have to make sure the input and seg volumes are in voxel
for voxel alignment
On 2/21/2024 4:30 AM, ERNEST KISSI wrote:
External Email - Use Caution
Hello freesurfer Team,
I have the grey matter segmentation from FSL and I have freesurfer
recon-all output but the
In what context? For fMRI, it is the signal change divided by the signal
mean (x100%)
On 2/20/2024 6:43 PM, Tina Zahrie wrote:
External Email - Use Caution
Hi all,
How is the percent signal change calculated within a ROI? What is the
formula for it?
Thanks,
Tina
I'm not sure what you are looking for as it is just the equation of a
gaussian. The PSF is given as the full-width-half-max. This is converted
to a std dev with
gstd = fwhm/sqrt(log(256.0))
On 2/18/2024 7:03 AM, Federica Di Antonio wrote:
External Email - Use Caution
Dear experts,
I cannot reproduce this locally. If you still want help, attach logs.
You can also try running it with -debug as the first option and capture
the copious terminal output.
On 2/6/2024 8:39 AM, Huang, Yujing wrote:
Not sure where this happened. Does it produce any log files that you
can
Sorry, don't know what VLSM is. Can you elaborate?
On 2/6/2024 3:19 PM, Martin Juneja wrote:
External Email - Use Caution
Dear FreeSurfer community and experts,
I would greatly appreciate any help/response with the following.
Thanks.
-- Forwarded message -
From:
On 2/6/2024 2:01 PM, Sarah Skinner wrote:
External Email - Use Caution
Question 1 - We found a few voxels that are labeled as the right
choroid-plexus, but it is nowhere near the rest of the structure. See
attached image. Is this a problem? If yes, what is the best way to fix
If you look in the recon-all.log file (or recon-all.cmd file), you will
find the command that creates the wmparc.mgz. You can adapt it to use
the DKT
On 2/6/2024 6:53 AM, Hamied Haroon wrote:
External Email - Use Caution
Hello Freesurfer Gurus,
Is it possible to obtain “wmparc”
the Torig = Norig. Here
Norig is acpc realigned.
Best,
- D
On Mon, Jan 1, 2024 at 4:27 PM Douglas N. Greve
wrote:
If you want to keep the original orientation, you can specify
--conform-dc. Would that fix your problem?
On 12/21/2023 9:30 AM, Dipterix Wang wrote:
Exte
Hi Lauri, that command does look right (and no need to worry about that
warning). The projfrac is the projection fraction. This is the distance
away from the white surface that fMRI will be sampled relative to the
thickness at that location. So a value of 0.5 means to sample in the
middle of
So, is the bottom line that when you run 7.4.1 on COS8 in parallel that
you get (slightly) different results each time?
On 2/2/2024 11:20 AM, Horn, Mitchell Jacob wrote:
Hi FS Devs,
I’m experiencing unreproducible thickness results when running any 7+
version with parallelization enabled.
Hi, no snapshots were attached.
On 2/1/2024 6:02 AM, Luisa Klahn wrote:
External Email - Use Caution
Hello!
I am processing structural data from a 3T scanner using Freesurfer
version 7.3.2. For some subjects, the grey matter looks very thin, and
the white matter looks overestimated.
Are you saying that synthseg itself is generating the wrong seg or that
something is going wrong further downstream? The recon-all stream with
synthseg is not a supported pipeline at the moment. For the standard
stream, can you send the full recon-all.log file?
On 1/29/2024 2:04 PM, Maya
you will have to binarize it first, eg, mri_binarize --i inputimage.mgz
--min threshold --o binary.mgz, then run mri_segstats --seg binary.mgz
--id 1 --i inputimage.mgz --sum sum.dat
On 2/7/2024 8:55 AM, Huang, Yujing wrote:
I think mri_segstats –i option will do that -
---
Date: Sat, 25 Nov 2023 14:04:08 -0500
From: "Douglas N. Greve"
Subject: Re: [Freesurfer] No ROI name in summary of MNI305 group
analysis
To:freesurfer@nmr.mgh.harvard.edu
Message-ID:
Content-Type: text/plain; charset="utf-8&quo
Currently, you'd have to convert them to t1-weighted images and then
run recon-all on that. I think there is software out there to do this if
you go the t1 maps from an mp2rage scan
On 1/25/2024 11:57 AM, AJ wrote:
External Email - Use Caution
Hi,
I have T1 relaxation maps over 4
See this tutorial
https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0 on
multimodal integration. Basically, you will need to run mri_vol2vol to
map your MPF volume to the anatomical/conformed space, then run
mri_segstats passing it the segmentation you want to use and the
Can you send the recon-all.log file that contains the error?
On 1/24/2024 4:01 AM, Kapteijns, Kirsten wrote:
External Email - Use Caution
Dear all,
I have run recon-all successfully on multiple subjects on multiple
timepoints. If I open the mri folder, it shows the correct talairach
The vol structure will reflect how the volume is stored on disk. If you
have two files that have the same structure (ie, order of rows, cols,
slices) then they will have the same vol in matlab regardless of the
header orientation.
On 1/23/2024 11:00 AM, Fotiadis, Panagiotis wrote:
Can you run it with -debug as the first option, capture the output, and
send it to me? It will be a lot of output, so just capture it in a file
and send the file, eg
preproc-sess -debug -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd
rest -per-run -sliceorder up -force | tee pps.log
is? Thank you so much!
Regards,
Xiaoxu
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Douglas N. Greve
*Sent:* Friday, January 19, 2024 3:16 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] FW: Create a Binarized ROI for Surface
On 1/19/2024 3: 45 PM, Na, Xiaoxu
On 1/19/2024 3:45 PM, Na, Xiaoxu wrote:
External Email - Use Caution
Dear Freesurfer Expert,
While the sphere can only be drawn using that Dr. Doug suggested, the
sphere option would mess up.
Do you need help with this? If so, can you give more info?
I have a further question
M, O'Neill, Alexandra Grace wrote:
Hi Doug,
Thanks so much for getting back to me. Below is our previous
correspondence:
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Date: *Friday, January 12, 2024 at 4:19 PM
*To: *freesurfer@nmr.mgh.harvard.edu
*Su
Sorry, I already forgot what the problem was. Can you include our
previous correspondence? Also, make sure to reply to the list. Thanks!
On 1/19/2024 10:07 AM, O'Neill, Alexandra Grace wrote:
Hi Doug,
Thank you for getting back to me. Unfortunately, the issue is
persisting, and the command
what is the wang atlas? volume or surface?
On 1/19/2024 12:20 AM, Sujeevini Sujanthan wrote:
External Email - Use Caution
Hi,
I would like to apply the wang atlas over the group activation maps
produced from Freesurfer analysis. I would appreciate any
guidance/instructions you can
That does not look like it is a problem with the input image. Do you
have a normal, invivo MRI that you can run samseg on to see if it is
just a problem with your platform?
On 1/18/2024 3:57 AM, K Eswar wrote:
External Email - Use Caution
Dear FS community
I have an ex-vivo human
The way I have done this was do compute T1w images (MPRAGE) through
simulations, then run recon-all on that.
On 1/17/2024 11:55 AM, Maksim Slivka wrote:
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Dear FS community,
Recently our lab started collecting 3D-QALAS (Cho et al., 2023). Using
this
if this would require a voxel wise analysis or
an ROI analysis… to my understanding this is more of a ROI analysis
between subjects - is this assumption incorrect?
Thank you,
Peter
On Sat, Jan 13, 2024 at 10:44 AM Douglas N. Greve
wrote:
So this is where I get confused on your intentions because
I would also be helpful to have some pics of what you are seeing. The
surface is not valid in the "medial well" -- ie all the non-cortical
structures on the central sagittial plane such as thalamus an VDC.
On 1/16/2024 7:50 AM, Huang, Yujing wrote:
Can you try the troubleshooting methods
...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Friday, January 12, 2024 4:26 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [External] Re: [Freesurfer] extracting measurements for
mean gray matter thickness/LGI
I don't understand. Why not use the mean thickness from FS? We have an
lGI module
,
Sorry I should have clarified. Yes, I would like to perform voxelwise
analysis of FA and MD values of hippocampal subfield between subjects.
Is this possible with free surfer?
Thank you again for your time.
M
On Fri, Jan 12, 2024 at 4:05 PM Douglas N. Greve
wrote:
oh, I thought you
, Jan 13, 2024, 12:31 AM Douglas N. Greve
wrote:
That is the bbregister command. You should look at the output of
recon-all
On 1/11/2024 5:37 PM, ERNEST KISSI wrote:
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This what the output shows doing the bbregister.
image.png
for each subject
onto the same space for inter subject analysis of FA values?
Thanks again,
M
On Fri, Jan 12, 2024 at 3:00 PM Douglas N. Greve
wrote:
Map the diffusion data to the subfield space, eg,
mri_vol2vol --mov fa.nii.gz --reg register.lta --targ
subfields.mgz --o fa
Choi wrote:
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Hi there,
Is there a way to successfully obtain FA/MD values from the
hippocampus subfields?
Thank you,
M
On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve
wrote:
I'm not sure what you mean. The subfields are an ROI-based
analysis
I suspect the problem is with the aseg.mgz input. You can regenerate
that with the new surfs with a different call to mri_surf2volseg.
However, that will take a --fix-presurf-with-ribbon argument, so you
will also have to regenerate the ribbon.mgz file for the new surfaces
with mris_volmask
You can try using mri_synthseg --i orig.mgz --o synthseg.mgz
it generally does a better job on cerebellum than the native FS command
On 1/5/2024 4:11 PM, Carlos Alcocer wrote:
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Hello,
Inferior portion of cerebellum are not segmented well. It is included
I don't understand. Why not use the mean thickness from FS? We have an
lGI module; we have not supported it in years, but maybe it still works.
https://surfer.nmr.mgh.harvard.edu/fswiki/LGI
On 1/10/2024 9:52 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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I'm not sure what you mean. The subfields are an ROI-based analysis. Are
you saying you want to do a voxel-based analysis (without reference to
ROIs)?
On 1/9/2024 12:05 PM, Mirsol Choi wrote:
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Hi there Freesurfer,
I am currently using freesurfer to take
I think v6 might be broken when using -bg. Try removing that.
On 1/8/2024 11:19 AM, O'Neill, Alexandra Grace wrote:
*Hello FS community,*
*
To correct for multiple comparisons for the results of a parametric
modulation GLM analysis, I have run mri_glmfit-sim using Freesurfer
version 6.0 with
please send the command line and the terminal output. Also, try using
tksurferfv (this is a wrapper around freeview that takes tksurfer-like
commands)
On 1/6/2024 8:59 PM, JAEHYUN KIM wrote:
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Hello,
I attempted to switch tksurfer to freeview in the
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