I'm not sure what to do about the medial surfaces. I don't think I've
run into that problem before. For the other issue, those areas are the
transverse sinus veins. In the next version, I have something that will
segment those areas. You can get it now in the dev version. Then run
mri_vsinus_se
I don't know, probably an open question. The change in resolution will
certainly affect results. Using the higher res (ie, not downsampling to
1mm) will likely give you the best result.
On 9/19/2024 10:38 PM, Jacob Bunyamin wrote:
External Email - Use Caution
Good afternoon,
I have
It is tricky but possible, but not might be worth it. You need to have a
whole brain segmentation, so you could superimpose the subfields onto
the aparc+aseg. You will need to create a color table for it (see
gtmseg.ctab after running gtmseg). You can then specify the new seg with
--seg to mri_
No, there is not an easy way to break it up that way. If you know some
programming, you could merge all 3 into one seg, then compute the PCA of
the coordinates, then divide it up along the largest direction
On 9/9/2024 1:54 AM, Necati Emre Şahin wrote:
External Email - Use Caution
De
Does it run with the --cpu flag? That will run it with the cpu and thus
isolate your problem to the gpu/cuda
On 9/9/2024 10:31 PM, Matthew Lynch wrote:
External Email - Use Caution
I run this command:
mri_synthseg --i /mnt/p/test/test-t2-3mm.nii --parc --robust --o
/mnt/p/test
an
The argument to the --s flag should be the name of the subject as was
specified when you ran recon-all, eg
recon-all -i t1_SPGR.nii -s subjectname -all
Then use dt_rcon -s subjectname ...
On 9/12/2024 7:45 AM, Ramesh Babu wrote:
External Email - Use Caution
Dear All,
I am new to dti
that could certainly be a problem. Is it really just a single value
throughout the brain? If so, that is the problem. On the other hand, it
could be that the freeview intensity limits are not set well, so try
playing with those. You can also click on voxels in the brain and look
at the values i
you have to pass it the file(s) you want to analyze. If you have a bunch
of dicoms, and your T1 is just one of many, you have to figure out one
of the files that corresponds to the T1. Or you can use dcmunpack, eg,
dcmunpack -src /path/to/your/dicoms -targ outputfolder -auto-runseq mgz
That comm
looks like it is only different in the first or second decimal place, is
that right? If so, then it is acceptable.
On 8/22/2024 4:11 PM, Sneha Pandya wrote:
External Email - Use Caution
Dear team,
A] I am running mri_gtmpvc on our data and need to extract stats data
that is in the s
On 8/13/2024 12:38 AM, WONG Wan Wa wrote:
External Email - Use Caution
Hi FS experts,
I want to do PET SUVR analysis using PetSurfer. When determining the
FWHM of the PSF of the scanner, is it the same value for Siemens
(Biograph40_mCT vs. Biograph128_mCT) or (Biograph64_Vision 600
You can add -cubic to the recon-all command line (though you might get
cubic at other times, but that probably won't hurt)
On 8/19/2024 1:40 PM, Jeiran Choupan wrote:
External Email - Use Caution
Dear Freesurfer support team,
I noticed that the interpolation setting used within the f
You can run something like
mri_convert nopvc.nii.gz --ascii nopvc.dat
This will give you a text file
To put a bunch together across subject, you can run something like
mri_concat */nopvc.nii.gz --o all.nopvc.nii.gz
Then do the same trick as above.
On 8/20/2024 12:01 AM, WONG Wan Wa wrote:
I'm not sure what you mean. Usually, one would edit the proper volumes
in freeview using the protocol described (eg, setting edited voxels to
certain values). One can implement automatic edits as long as one keeps
to the protocol.
On 7/30/2024 5:09 PM, Edwards, Vincent wrote:
Externa
ow if more information is needed! Thanks so much!
Best,
Tengwen
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, July 29, 2024 12:26 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Su
please send your command line, terminal output, and stats file
On 7/23/2024 3:07 PM, Selena Gangaram wrote:
External Email - Use Caution
Hi,
I hope you are doing well, I subscribed to your mailing list to ask my
question!
I was wondering if you knew the reason as to why my extracti
please send the recon-all.log file in the scripts folder
On 7/23/2024 2:14 PM, Tengwen Fan wrote:
External Email - Use Caution
Dear FreeSurfer Developers,
I hope this email finds you well!
I am using fMRIprep to do pre-processing. The fMRIprep combines
methodology from AFNI, ANTs, F
You can try mri_seghead and/or mideface (which uses mri_seghead)
On 7/16/2024 6:27 AM, Francesco Lomi wrote:
External Email - Use Caution
Hi everybody,
Do you know how to create a scalp mask file with freesurfer?
Thank you in advance
Francesco
___
Sorry, there is nothing here (ie, no fsgd file, no images). Did you mean
to attached?
On 7/10/2024 5:31 AM, Josefine Tingdal Taube Danielsen wrote:
External Email - Use Caution
Hi Freesurfer support,
I'm using Freesurfer version 7.4.1 and Ubuntu 22_x86_64.
freesurfer-linux-ubuntu22_
in FS, all the voxel indices are >= 0
I don't know what the numbers mean you put below
On 7/15/2024 6:35 AM, ERNEST KISSI wrote:
External Email - Use Caution
Dear fresurfer team,
Please I want to extract the intensity of a voxel 48, -56, -34. But
my voxel ranges of my image does not
m that occurred.
Best,
Danilo
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Sunday, July 14, 2024 4:56:22 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesur
You'll have to create curvature files, inflate the surface to a sphere,
then run mris_register
On 7/10/2024 10:10 AM, Stefano Delli Pizzi wrote:
> External Email - Use Caution
>
> Dear,
>
> We are using the Magicc Maps (https://github.com/kwagstyl/MAGICC). The maps
> are in fsLR system
what you are showing there is not a segmentation error but a severe
misalignment. What is your freeview command line? Are you sure that the
anatomicals and the surfaces are from the same subject?
On 7/10/2024 4:59 AM, Tornabene, Danilo wrote:
External Email - Use Caution
Dear FreeSur
Have you looked at the individual subjects? This will sometimes happen
when there are strong global signals as the global signal (by
definition) gets into the regressor and is everywhere, so you end up
with these large swaths of positive activation. You're already doing the
things I would sugge
you can also use fscalc, which is a frontend for mris_calc
On 7/9/2024 3:14 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
Perfect thank you
On Tue, Jul 9, 2024 at 1:30 PM Huang, Yujing
wrote:
Is this what you are looking for?
https://surfer.nmr.mgh.harvard.edu/p
I think you can use any picture you want without permission.
On 7/8/2024 7:14 AM, ALARIO Francois wrote:
External Email - Use Caution
Hello
I am considering using freesurfer-generated images not in a scientific
paper but in a popular science book (commercial).
What is the preferred
That is the way I would have suggested. Does it run to completion when
you use the softlink? Reorganizing the folder structure it likely to
break a lot of things.
On 7/11/2024 10:02 AM, Sneha Pandya wrote:
External Email - Use Caution
Dear team,
I am running mri_gtmpvc using RBV cor
On 7/3/2024 7:19 PM, Hickman, Leonard B. MD wrote:
External Email - Use Caution
Hello all,
I am using FreeSurfer to measure specific cortical parcellations and
subcortical segmentations in a medium-sized dataset (over 150 scans).
About a fifth of the scans include cortical lesions
It is not normalized. these are volumes, surface ares, and thicknesses
of various regions. I'm not sure what common space corrections you could
do. You can correct for eTIV
On 7/3/2024 1:11 PM, PATRICIO FELIPE RIQUELME wrote:
External Email - Use Caution
Hi everyone.
I just began to
On 7/1/2024 1:05 AM, Bronwyn Overs wrote:
External Email - Use Caution
Hi Freesurfer Mailing List,
I work on a large bipolar disorder imaging study that has been running
for over 10 years. We previously acquired 2 sMRI time-points (pre
2013, /n/~500, /n/~250 at each time-point) on
Have you seen this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
On 6/28/2024 9:48 AM, Emma Harper wrote:
External Email - Use Caution
Dear Freesufer teams,
Does anyone have any recommendations to correct for alpha inflation
when doing the mul
have suggestions?
Thanks,
Alice
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, June 27, 2024 12:36 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] FreeSurfer atlases
I'm not sure wha
It can't find the file struct.nii. You have to give it the full path to
the file. It looks like $Users is not set to anything (blank)
On 6/28/2024 12:03 AM, Lydia Luck wrote:
External Email - Use Caution
Hello-
I am trying to do recon-all on my brain MRI and I’ve rewritten it so
man
files of
recon-all -all command.
Best,
*发件人:* freesurfer-boun...@nmr.mgh.harvard.edu
代表 Douglas N. Greve
*发送时间:* 2024年6月27日 6:35
*收件人:* freesurfer@nmr.mgh.harvard.edu
*主题:* Re: [Freesurfer] The file absence problem of the
I'm not sure what you mean. We don't have an image of the subfields in,
eg, mni space. Usually, you just run the subfield seg on the data that
you want subfields for
On 6/26/2024 7:58 AM, Savoia, Alice (Stud. FPN) wrote:
External Email - Use Caution
Hello,
I am looking for a freesufe
that has to be created with a separate process (mri_seghead)
On 6/26/2024 2:11 PM, Quanjiang Liu wrote:
External Email - Use Caution
Hi, I ran the recon-all -all command successfully. But the
lh.seghead and rh.seghead didn't appear in my output folder. The
attachment is the process
the image
seems warped.
Thank you,
Best Wishes,
Gaurav Ambwani.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Tuesday, June 25, 2024 9:51 PM
*To:* freesurfer@nmr.mgh.harvard.edu
ome reason it isn't working.
I hope that this clarifies what I was trying to do.
Thank you,
Best Wishes,
Gaurav Ambwani.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday,
It will take all edits you have made into account when you rerun it.
On 6/25/2024 1:00 PM, Blujus, Jenna wrote:
External Email - Use Caution
Hi all,
I have processed a set of T1w data through recon-all (v7.3.2) and am
now making manual edits, if necessary. I have had a few cases wher
On 6/24/2024 6:47 PM, Andrew Jahn wrote:
External Email - Use Caution
Hello,
I have a raw anatomical image called raw.mgz, which I have manually
annotated using Freeview; the resulting annotations are saved in a
file called seg.mgz. I want to compare this to the annotations
automa
Fill holes and normalize
> fslmaths ANTS_43Kids_template_rigid2MNI.nii.gz -bin -fillh -mul
> ANTS_43Kids_template_rigid2MNI.nii.gz -div $(fslstats
> ANTS_43Kids_template_rigid2MNI.nii.gz -P 100) -range
> ANTS_QS_template_MNIS.nii.gz -odt float
>
> Thank you so much!
>
> Best regards,
&
> # Fill holes and normalize
> fslmaths ANTS_43Kids_template_rigid2MNI.nii.gz -bin -fillh -mul
> ANTS_43Kids_template_rigid2MNI.nii.gz -div $(fslstats
> ANTS_43Kids_template_rigid2MNI.nii.gz -P 100) -range
> ANTS_QS_template_MNIS.nii.gz -odt float
>
> Thank you so much!
>
I don't think she was responding to your question but rather to that of
Ernest
On 6/21/2024 1:23 PM, Gaurav Ambwani wrote:
External Email - Use Caution
Dear Yujing,
I don't think that this was my question. Here are the contents of what
I sent in my previous email:
I took a 1mm T1
Sorry, I'm not sure what the problem is that you are describing. I see
from the recon-all file that
MNI_freesurfer_T1.nii.gz is your input. What is that? Is that after skull
stripping? Why not just give it the full head?
On 6/20/2024 3:52 PM, Gaurav Ambwani wrote:
External Email - Us
This can be a little tricky. Some information gets embedded into the
files (you won't find this with a text search). You can generally see it
with mri_info (mgz files) or mris_info (surface files)
However, mri_info can print out info that is not in the file but just
relates to the location of
You can also use mri_mask, eg, after running synthstrip, eg
mri_mask -bb 0 stripped.mgz stripped.mgz stripped.crop.mgz
-bb 0 means to create a tight (0) fitting bounding box around the
non-zero voxels. The output stripped.crop.mgz will be the cropped output
On 6/18/2024 11:00 AM, Huang, Yujing
ocess.
Is this approach (specify -synthseg only for the CROSS recon-all)
appropriate for longitudinal processing?
On Mon, Jun 17, 2024 at 10:21 AM Douglas N. Greve
wrote:
Yes, that is the problem, not a lot of great options. One thing
you could try is to run synthmorph to create the
-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, June 3, 2024 6:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] How to get the parcellations to the
initial space as before running recon all
Does this web site
https://surfer.nmr.mgh.harvard.edu
Yes, that is the problem, not a lot of great options. One thing you
could try is to run synthmorph to create the m3z.
On 6/10/2024 2:36 PM, Dan Levitas wrote:
External Email - Use Caution
Hello,
I am following the longitudinal freesurfer pipeline
(https://surfer.nmr.mgh.harvard.ed
I'm not sure what you mean, but I don't think we output this
information. You can probably do it yourself in matlab or python
On 5/21/2024 12:26 PM, Jingjing Liu wrote:
External Email - Use Caution
Dear Freesurfer team,
I am looking for the answer that where I can find the document of
Here on the FreeSurfer list, we don't know much about the FSL tools like
BIANCA. Why don't you post to the FSL group?
On 6/12/2024 2:51 PM, CRISTIAN MOJICA wrote:
External Email - Use Caution
Hello,
I will be running BIANCA in FSL after some quality control with the
requisite files
In fsfast, the censoring is done in the analysis by creating a tpexclude
file and specifying this file when running mkanalysis-sess. Below is a
snippet from the mkanalysis-sess --help
-tpexclude tpxfilename
This is the name of a time point exclude file (TPEF) used for removing
outliers in th
It is not PVC corrected. To do that, you'd have to use the --mgx or --rbv
Note that doing voxel-wise PVC is tricky because you have multiple
tissue types in each voxel. So you can keep the same resolution but
then you have to represent only one tissue type (mgx) or you have to
create a higher
The lh.area in fsaverage is the area of the white surface (as in an
individual subject). But the white surface is not like an individual in
that many of the folds have been smoothed out (because it is an
average). So mri_surfcluster fixes this internally, which is why you see
the discrepancy (a
We do not offer anything special for this. The difference in group size
is not an issue in and of itself. The only problem that would arise is
if the groups have different variances.
On 5/18/2024 12:07 PM, std...@virgilio.it wrote:
External Email - Use Caution
Hi
I’m using fs-fast t
Mostly these:
https://pubmed.ncbi.nlm.nih.gov/15501102/
https://doi.org/10.1016/S0896-6273(02)00569-X
For a separate fornix seg, see
https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic
On 5/22/2024 1:34 PM, Ahsan Ali wrote:
External Email - Use Caution
Hello everyone,
Could anyone
The -c means to "conform". In addition to changeing it to 1mm iso, it
will change the data type to uchar. Uchar only has 8 bits, so it does an
intensity rescaling to make sure all the intensities fit in this range
On 5/22/2024 12:55 PM, ERNEST KISSI wrote:
External Email - Use Caution
This usually means that there is a large difference in the geometry
between time points eg, the voxel size has changed substantially. If you
want more help, make sure to include the recon-all.log file
On 6/7/2024 7:45 AM, Yasmine Salman wrote:
External Email - Use Caution
Dear FreeS
Sorry, I can't understand from you description what is going wrong. How
do you know that something is off? Can you list your command lines?
On 6/6/2024 8:22 PM, O'Dor, Sarah wrote:
We are trying to run resting state connectivity analyses using
amygdala ROI. The left hemisphere ran fine, but f
That should have worked, but I would use the method on this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 6/6/2024 4:07 PM, Nina Rouhani wrote:
External Email - Use Caution
hello!
after freesurfer segmentation (through fmriprep v23), i converted the
aparc+as
Can you send us the terminal output? Can you point us to the data on the
network so that we can recreate? @YH - can you take a look?
On 6/6/2024 3:56 PM, Iglesias Gonzalez, Juan E. wrote:
Dear FS experts,
We get a segfault when I try to resample images with the command:
mri_convert input.mgz
If it is only one subject and you have no continuous variables, you can
do it that way. If you have continuous variables, you will need to use
DOSS (different-offset same slope) to force the slopes to be the same
across classes (because you can't compute a slope from a single data point)
On 5/
n case of any clue? Thank you so much!
>
> Best,
> Chen
>
>
>
> - Original Message -
>> From: "Douglas N. Greve"
>> To: "freesurfer"
>> Sent: Wednesday, 29 May, 2024 15:26:25
>> Subject: Re: [Freesurfer] Recon-all for a common temp
Does this web site
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat cover
what you need to do?
On 6/3/2024 10:58 AM, Reji, A. (Amal, Student M-EE) wrote:
External Email - Use Caution
Hi,
I was trying to get the mesh files for cortical parcellations
after running re
sounds like something is wrong with the image. Did you look at
ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a
head?
On 5/28/2024 6:07 AM, Chen Yang wrote:
> External Email - Use Caution
>
> Hi everyone,
>
> I tried to run the reconstruction with the command line:
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:
Exter
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 already
e you 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 an
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
__
erence.
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 sti
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 subcor
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:
Ex
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 currently
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 average
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 area
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 f
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 would
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
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 how
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 cerebel
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 li
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 n
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
out
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 tr
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*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:
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Dear FreeSurfer Experts,
Sorry, I think I've found the answer. It's because Jacobian correction
was performed for mris_preproc, right?
To
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
tried 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, Ma
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:
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Hello,
So I ran FreeSurfer to get numeric data from MRI images and got these
files under the stats page.
Screenshot 2024-03-18 144107.png
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:
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Hi experts,
As stated in the subject, can kinetic modeling be applied to PET data
Thank you 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-se
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 a
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 se
!
Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve
ha scritto:
entire terminal output
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The information in this e-mail is
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:
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Hello FreeSurfer Experts!
I’m having trouble projecting the Yeo 17n annotation to volume space.
I’ve tried on FS v7.
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