Use both -autorecon1 and autorecon2-cp
On 9/2/2022 8:27 AM, Mostafa Fakhri wrote:
External Email - Use Caution
Hi there,
I need just wm.seg.hgz image therefore I used autorecon2-cp:
recon-all -sd /share/users/mfakhri/freeSurfer-analys/subjects -subject
102109_3T -i
please include previous emails, otherwise I won't know what "I believe
so" refers to
On 9/1/2022 3:45 PM, Trolle, Carl wrote:
Hi,
I believe so, I ran the following commands:
mris_register -L
subject/label/?h.central_sulcus.label $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs
You can also try segment_subregions. This is a python implementation
that gives almost exactly the same result (but limited to T2). See
https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation
It should run on Mac
On 8/31/2022 11:28 PM, fsbuild wrote:
External Email - Use
code self as 2
and non-self as 1 so that condition 2 (self*valence) would be
different from condition 5 (valence ratings only)?
Incredibly helpful, Doug- thank you so much!
*From: * on behalf of "Douglas
N. Greve"
*Reply-To: *Freesurfer support list
*Date: *Tuesday, August 30, 20
of the brain.
Thanks,
Miriam
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Sunday, August 28, 2022 4:13 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] sclimbic
mri_cc. Look in the recon-all.log file for an example command line. You
may want to change the output file so that you do not overwrite what is
there.
On 8/31/2022 9:56 AM, Sam W wrote:
External Email - Use Caution
Hi Bruce,
Thank you for the response! Which freesurfer command do I
I don't think the brain.mgz is the right one to look at as it has
already been partially segmented. Compare against the norm.mgz (or
nu.mgz) instead. It is really hard to determine where the lateral
boundaries are in thalamus
On 8/31/2022 2:46 AM, Thalhammer, Melissa wrote:
External
There is not enough information to understand what you did in #2
On 8/30/2022 3:56 PM, Ruifeng Dong wrote:
External Email - Use Caution
Hi all,
I am computing volumetry using freesurfer using two different runs.
1. I just use recon-all -all, and then look at the aseg.stats file.
2.
I think it should work for b0 images, but I would avoid using any frames
that have a gradient. Note that you will need about 10 images to compute
the fwhm using mri_fwhm (also make sure you use a mask)
On 8/30/2022 1:33 PM, Igor Nestrašil wrote:
External Email - Use Caution
Dear
Hi Dilek, your bug report is incomplete. Please see
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for how to file
an informative bug report.
On 8/30/2022 12:51 PM, Dilek Özkan wrote:
External Email - Use Caution
Hello dear all,
I use Freesurfer-Samseg for MS lesion
associated with the contrast
for -a 3 and the contrast for -a 4 would be the same for trials that
subjects rate as 1 (self-relevant) vs 0 (not self-relevant)? Could we
code it as 2 (self-relevant) and 1 (not self-relevant)?
Many thanks!!
*From: * on behalf of "Douglas
N. Greve"
I don't think you can. I have not looked at combat in a long time, but I
thought they did their own GLM. combat might take a design matrix, in
which case you could use mri_glmfit and your FSGD to create the design
matrix.
On 8/30/2022 9:37 AM, Rene Seiger wrote:
External Email - Use
If you resample the t1 to another space, it might get blurrier.
On 8/30/2022 9:46 AM, Dilek Özkan wrote:
External Email - Use Caution
I decided to register T1 and Flair to DIR at the beginning. with this
way, I will get the new mask in already DIR's space which means
manually
If you want to use FSL, you will have to convert to nifit, eg,
mri_convert file.mgz file.nii.gz
On 8/30/2022 7:01 AM, Dilek Özkan wrote:
External Email - Use Caution
Hello dear all,
I want to use Freesurfer-Samseg for MS lesion
segmentation(cross-sectional).
I got the T1 and
t at back and nose) also seems to be the case with
participants that sclimbic did work on..
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Tuesday, August 9, 2022 10:34 PM
*To:* freesurfer
’m not clear how to get the main effect of valence (brain
regions that scale with increasing emotion valence, while holding
self-relevance constant)?
*From: * on behalf of "Douglas
N. Greve"
*Reply-To: *Freesurfer support list
*Date: *Sunday, August 14, 2022 at 1:37 PM
*To: *"
We did fix this at some point. Can you try running the 7.3 version to
see if you get the same results? Often multiple threads will yield
different results unless specifically programmed otherwise.
On 8/27/2022 4:41 AM, Giulio Siracusano wrote:
External Email - Use Caution
Hi
multivariate lonitudinal atrophy models on the data and need to
separate i.e. frontal from parietal cortex.
Best Regards Matthias
*Von:*freesurfer-boun...@nmr.mgh.harvard.edu
*Im Auftrag von *Douglas N. Greve
*Gesendet:* Freitag, 24. Juni 2022 16:22
*An:* freesurfer@nmr.mgh.harvard.edu; Cerri
Not sure what you are asking or saying. Is Synthseg not useful for gad
images or is it useful?
On 8/25/2022 10:54 AM, Gonzalo Rojas Costa wrote:
> External Email - Use Caution
>
> Hi:
>
>SynthSeg is useful for T1-GD volumetric images? Another algorithm,
> software?
>
>
Since this is longitudinal, I'm assuming that your contrast is actually
something like contrast C = (INT2-INT1)-(CON2-CON1) where 1 and 2 the
the time points. As you suggest, both (INT2-INT1) and (CON2-CON1) might
both be less than 0, but if INT is less negative than CON, then C will
be
I'm not sure what you mean by "inflate" here. Do you just mean to run
recon-all? Usually, you would run recon-all, then run segmentHA, then
register the fMRI to the anatomical (bbregister), then map the segs to
the fMRI space (mri_label2vol), then run something like mri_segstats
--seg
which version of FS are you using? There was a bug in pre 7.3.2 versions.
On 8/20/2022 11:05 AM, Fischl, Bruce wrote:
Hi Carl
Can you upload your subject including the central sulcus labels you drew?
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Trolle, Carl
you can also
Convert a surface file to ascii (vertices are surface normals):
mris_convert -n lh.white lh.white.normals.asc
On 8/20/2022 8:41 AM, Yendiki, Anastasia wrote:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki/SurfaceNormal
The "Mean" column will be the mean lGI in the region
On 8/17/2022 4:42 AM, Steger Celine wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I try to explore the Gyrification Index of both hemispheres in a
population. For this I computed the LGI using the Freesurfer
Are you trying to run this from outside of recon-all? If not, can you
send the recon-all log file? Also, have you looked at the talairach
registration?
On 8/15/2022 7:50 AM, 丁晴 wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to generate filled.mgz
)
And then create a contrast of 2 vs 4 to test the interaction? Would
testing contrast 1 vs 0 be a test of the main effect of self-relevance
and contrast 3 vs 0 the main effect of valence?
Thanks so much for your help!
Angela
*From: * on behalf of "Douglas
N. Greve"
*Reply-To:
Yes, look at the ROI analysis tutorial (eg, asegstats2table or
aparcstats2table then mri_glmfit with the --table option)
On 8/13/2022 2:22 AM, Hye Min Shin wrote:
External Email - Use Caution
Hello experts,
While going through GroupAnalysis tutorial for freesurfer
(*MailScanner has
at back and nose) also seems to be the case with
participants that sclimbic did work on..
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Tuesday, August 9, 2022 10:34 PM
*To:* freesurfer
?
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Tuesday, August 9, 2022 10:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left
Can you send the terminal output and the petsuv.segstats.dat? How have
you verified that the registration is correct? What version of FS are
you running?
On 8/5/2022 4:44 PM, Bouchra Guelib wrote:
External Email - Use Caution
I want to segment registered PET to T1 MRI to 45
not sure. Try running
mri_sclimbic_seg --i GP0050/mri/orig.mgz --o junk.mgz
On 8/4/2022 4:20 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi all,
I am receiving this error when trying to run sclimbic module. It's not
being very descriptive
Try mergeseg. Run with --help to get more info
On 8/3/2022 3:41 PM, Benjamin Deck wrote:
External Email - Use Caution
Hi there,
I have extracted an ROI mask for the subthalamic nucleus from MNI
space and registered this with the subject's native space orig.mgz
I would like to
If I understand correctly, you have one site that acquires two scans,
one sag and one axial, and you want to register them together and
compute the average, then feed the average to recon-all? Do they have
the same isotropic resolution? I'd guess that this would create a
systematic artifact.
looked ok after that.
On 7/28/2022 8:58 PM, Miriam Taza wrote:
Nothing strange about them.
They’re T1w scans 1x1x1mm3
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, July 28
If you are going to pass it the UNI, then you will probably need to mask
out the stuff outside of the head. One way to do this is to run samseg
on the INV1 or INV2 (INV1 probably better), the run
mri_mask uni.mgz seg.mgz uni.masked.mgz
Then pass uni.masked.mgz to recon-all
On 8/2/2022 8:39 AM,
Hi, at long last we have an official release of 7.3. See the release
notes can be found here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes and also copied
below. Thanks to all who tested the beta version.
best
doug
* Bug fix when converting diffusion tensor data with a negative
Can you send us a sample case?
On 7/28/2022 8:58 PM, Miriam Taza wrote:
Nothing strange about them.
They’re T1w scans 1x1x1mm3
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent
those look like hcp commands so you should contact them
On 7/28/2022 2:00 PM, Ariana Fei wrote:
External Email - Use Caution
I'm attaching a list of command I used to convert freesurfer cortical
thickness output to native space:
$Caret5_Command -file-convert -fsc2c
here a log?
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, July 28, 2022 1:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] etiv value differs if u
ers a bit from the median, sclimbic module
calculates etiv to an extreme.
Is this expected to happen? I am concerned if my volumes are incorrect.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Gr
Have you looked at the input volume to see if there is anything strange
about them? What kind of scans are you passing to it? What is the
resolution?
On 7/25/2022 9:03 PM, Miriam Taza wrote:
External Email - Use Caution
Hello,
I noticed 20 out of ~240 subjects left basal forebrain
Yes, see
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation
On 7/25/2022 6:56 PM, Angela Fang wrote:
External Email - Use Caution
Hi Freesurfer community,
I have run participants through an event-related fMRI task in which
subjects rate whether trait adjectives
how are you converting them?
On 7/27/2022 11:20 AM, Ariana Fei wrote:
External Email - Use Caution
Hi,
We are recently trying to get cortical thickness from freesurfer and
converting them to 32k. A problem we notice is that after converting
to 32k, all the cortical thickness values
I usually just divide the volume by the eTIV (you can do this in
asegstats2table with the --etiv flag). Some people will use it as a
nuisance regressor in the GLM
On 7/27/2022 3:11 PM, Bouchra Guelib wrote:
External Email - Use Caution
-- Forwarded message -
De :
26o%3Dnewest>
Douglas N. Greve
<https://secure-web.cisco.com/1ihiy9xLc9u1yyF8DQ1uOVgvZt_RRMNCUkxXo527aY3PFbUXS3sfC31bcx11dGxVlTccZYSThLDEdA1-3FGQ1CRTg7XrTBcJhZLLtaE0sj3xsYQuQhsTIcoXEHc80x65wcAwmwzAQhBjtjU7gSRcvRovhlCWIQpbERg4NaELK39aLmAdyzCW6rcv0uS1vZXVVEKZpjbIClaZc0KvKcon0XBFT2EnE8V8WnmbZFA0Ms_Aj
I'm not sure what is going wrong with that. Can you look at the data?
Particilarly the norm.mgz
On 7/26/2022 9:53 AM, gianrocco wrote:
External Email - Use Caution
Hi,
I attache hereby my email, as it was rejected — since I was not
registered yet to the list
Thanks again
Kind
website, I
found that changing the space is a step of the recon-all, so I used
recon-all directly on my original data without any space changing.
Thank you so much for your answer.
Le lun. 25 juil. 2022 à 03:40, Douglas N. Greve
a écrit :
did you see where it said "see *MailScann
yes, that is the correct interpretation
On 7/16/2022 1:00 PM, Boa Sorte Silva, Narlon wrote:
External Email - Use Caution
Dear experts,
I am conducting a group analysis and wanted to confirm that the set up
below accurately addresses our research question. Thanks for your
help,
, then it complains
interreg: Undefined variable.
When I added interreg = 5, then it complains
subj: Undefined variable.
Should I continue fixing it until no more Undefined variable?
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Douglas N. Greve
*Sent:* Monday, July 25, 2022 5:42 PM
.mgh.harvard.edu
*On Behalf Of *Douglas N. Greve
*Sent:* Monday, July 25, 2022 5:02 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
are you sure the config file is right? it should be defining the
intrareg variable
On 7/25/2022 2:11 PM, kingwai
if my volumes are incorrect.
I don't know what you mean. The eTIV in mri_sclimbic_seg should agree
nearly perfectly to that in aseg.stats
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent
: Undefined variable.
Thanks,
King-Wai
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Douglas N. Greve
*Sent:* Monday, July 25, 2022 1:55 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
Can you copy the attached trac-preproc
Can you copy the attached trac-preproc into $FREESURFER/bin and try
again (after removing the link)?
On 7/22/2022 8:36 AM, kingwai@gmail.com wrote:
External Email - Use Caution
Hi Anastasia,
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all,
did you see where it said "see
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
I cannot replicate this on my data. The differences are rather extreme
(factors of 3). Can you get us access to the one with the largest
difference? YOu can also try regenerating the aseg.stats file, eg,
cd subject/
mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/redo.aseg.stats
--pv
The ?h.sphere.reg xyz coordinates are coordinates on the sphere. To
apply a spherical registration, a point on one spherical mesh is mapped
to the closest point on the other spherical mesh. not sure if that
answers your question ...
On 7/21/2022 5:26 PM, Salar Dini, Elaheh wrote:
If you have the x virtual frame buffer installed, you can run freeview
via fsxvfb and it will write your screen shots to a file without
bringing up an image (thus the virtual frame buffer). This is available
in 7.3
On 7/20/2022 12:40 PM, Garikoitz Lerma-Usabiaga wrote:
External
The sig.table.dat has the sig values in it (ie, -log10(p)*sign). The
gamma.table.dat will have the contrast values. These are NOT percentages
but have the units of the input y table.
On 7/20/2022 9:18 AM, Carolina Ferreira wrote:
> External Email - Use Caution
>
> Hi, I'm using the
Why not just add the volumes across the hemis?
On 7/19/2022 9:38 PM, Mohanad Arafe wrote:
External Email - Use Caution
Hello,
I am attempting to measure the gray matter volume (mm^3) of the
insula. After getting all of my labels, I performed the following
operations to merge the
That is pretty small, at least in that picture. It could be that they
are not really overlapping as freeview has to project the surfaces into
the plane and that brings some inaccuracies with it. If they are really
overlapping, it is so small that I would not worry about it.
On 7/19/2022 1:35
nch3/P040008_MR_v01/surf/rh.pial:edgecolor=255,0,0:edgethickness=1:name=rh.pial_r3
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Sunday, July 10, 2022 2:05 PM
*To:* freesurfer@nmr.mgh.harvard.e
you very much,
Adriana
On Jul 10, 2022, at 5:56 PM, Douglas N. Greve
wrote:
I'm having problems following your narrative. Can you send the fsgd
and contrast files?
On 7/4/2022 5:37 PM, Adriana Cannizzaro wrote:
External Email - Use Caution
Hello Freesurfers,
We performed
The scout is a short, low resolution scan used by the scanner operator
to set the field of view for later scans; it is not use ful.
The SpinEcho looks like it is part of a functional or diffusion sequence
to perform B0 distortion correction (so not used in the anatomical analysis)
I don't know
What was your mri_vol2surf command?
On 7/14/2022 4:59 AM, Alberto Del Cerro Leon wrote:
External Email - Use Caution
Hello Freesurfer Team, I am trying to use a ROI to create a label into
fsaverage. Once I registered my ROI to the fsaverage space I performed
a mri_vol2surf and
You have to tell it to do something, eg, add -all to the command line
On 7/13/2022 11:53 PM, Zixuan Lin wrote:
External Email - Use Caution
Hello!
I am trying to run recon-all but it only converted the original image
to .mgz and finished without error. I checked all other folders
Why don't you post to the FSL list?
On 7/13/2022 4:19 PM, Arman Avesta wrote:
External Email - Use Caution
Hi gang,
I want to use fslreorient2std to reorient my NIfTI files in the
standard MNI format. I tried:
fslreorient2std T1.mgz
fslreorient2std -file T1.mgz
fslreorient2std
You can use the per-vertex regressor (--pvr) in mri_glmfit. There is
currently no way to correct this for multiple comparisons though.
On 7/13/2022 10:53 AM, Silva Rudberg, Jason wrote:
External Email - Use Caution
Hello Freesurfers,
I am trying to conduct a vertex-wise comparison
There is not a way to do this automatically as part of recon-all. You
would need to build a new gca by labeling a set of subjects then
building the gca with gcatrain.
On 7/12/2022 1:00 PM, Ramtilak Gattu wrote:
External Email - Use Caution
Hello all,
We built a CC mask with 3
There is not a sulcal CSF measure in the aseg. You can run samseg --i
orig.mgz --o samseg to get a measure of the sulcal CSF (in the "CSF"
segmentation)
On 7/12/2022 4:57 AM, Michele GRASSO wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
My name is Michele Grasso
Pick a hemisphere (either lh or rh). Also, you should verify that your
volume overlays on fsaverage correctly with something like
tkmeditfv fsaverage orig.mgz -surfs -fminmax .01 1 -ov
rReslice_Combined_roi_meanRD.nii -reg
$FREESURFER_HOME/average/mni152.register.dat
On 7/11/2022 6:23 PM,
registration from header.
Using /home/developer/template/template_RW.nii/mri/orig.mgz as
target reference.
error: mghRead(/home/developer/template/template_RW.nii/mri/orig.mgz,
-1): could not open file
Am I setting the registration incorrectly?
Thank you again!
Rachel
*From: *Douglas N. Greve
Have you looked at the images in freeview to verify that they both look
ok (eg, one is not all 1s or 0s or missing half the brain or
misoriented)? Can you try to run it with the unmasked data as a test?
On 7/4/2022 4:24 PM, Andrew Beaudin wrote:
External Email - Use Caution
Hello
Not sure what is happening. Does it work if you restart the long time
point from scratch (ie, remove the folder that is there)?
On 6/29/2022 5:49 PM, coope...@student.unimelb.edu.au wrote:
External Email - Use Caution
Dear FreeSurfer developers,
I’m attempting to run recon-all with
, how would the pseudocode differ for
sig.cluster.mgh vs sig.voxel.mgh?
Thanks,
Mark
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Sunday, June 19, 2022 10:37 AM
*To:* freesurfer
First, what is rReslice_Combined_roi_meanRD.nii? How was it created? If
that is you lesion map, then it is not the right input to BBR. I can't
remember, but if the AAL is in the MNI152 space, then it will be easier
to just run recon-all on the MNI152 ( or whatever the atnatomical
reference is
You can use ces/rstd
On 7/5/2022 10:50 AM, Caspar M. Schwiedrzik wrote:
External Email - Use Caution
Hi!
I would like to compute Cohen's D for individual subjects.
I was wondering whether I can use the output from selxavg3-sess for
this: ces./rstd
Or does this only work with gamma
I'm having problems following your narrative. Can you send the fsgd and
contrast files?
On 7/4/2022 5:37 PM, Adriana Cannizzaro wrote:
External Email - Use Caution
Hello Freesurfers,
We performed a whole-brain analysis using general linear model
analysis with FreeSurfer mri_glmfit
These dof files are created by selxavg3-sess. If they are not there,
then that program must have failed in some way
On 6/29/2022 4:10 PM, Shapiro, Noah Lorenz wrote:
Hi Paul,
Thanks for your suggestion.
I examined all files within the /script directory from recon-all from
two subjects where
tksurfer is depracated. Try using tksurferfv instead
On 6/29/2022 4:33 PM, Rachel Wagner wrote:
External Email - Use Caution
Hello,
I am attempting to paint my spm functional data onto freesurfer’s
anatomical image.
I ran this code: tksurfer bert lh inflated -overlay updated.img
Maybe it is running out of memory? Can you try it reducing the number of
inputs?
On 6/29/2022 2:42 PM, Benjamin Deck wrote:
External Email - Use Caution
Hi there,
I am attempting to concat a number of volume files that are filled
cortical ribbons from a series of label files.
My
what are you using as input? I can't tell from the image you sent, but
it looks pretty blurry. What is the resolution? What kind of acquistion?
On 6/28/2022 11:38 PM, Wang, Yu wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I used the _recon-all -s c1NT816 -i
Sorry, orig.mgz should exist in mri not mri/orig
On 7/10/2022 4:04 PM, Douglas N. Greve wrote:
Does orig.mgz exist in /usr/local/freesurfer/7.2.0/subjects/home/mri/orig?
Also be aware that we are phasing out register.dat files in favor or
using lta files. Also, the tk tools (tkregister2
Does orig.mgz exist in /usr/local/freesurfer/7.2.0/subjects/home/mri/orig?
Also be aware that we are phasing out register.dat files in favor or
using lta files. Also, the tk tools (tkregister2, tkmedit, tksurfer) are
officially depricated. Try using tkregisterfv instead.
On 6/28/2022 4:38 PM,
.
Thank you so much!
Sarah
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, June 27, 2022 10:18 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] aseg.presurf
information that would be useful to
send along or if I should send anything again in a different format.
Thank you so much!
Sarah
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday
Have you seen this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 7/7/2022 12:18 PM, Yiyu wrote:
External Email - Use Caution
Thank you, Bruce
If possible, I would like to transform an individual coordinate
(x,y,z) from FreeSurfer space to the native space.
Can you send us the data? Just one case with a copy of the original data
and a copy of the data where you reran recon-all but it did not protect
the edits. Also, send a freeview command line that will load up the two
volumes and the col, row, slice of a location where there were edits in
the
15:32, Douglas N. Greve
a écrit :
This is not the workflow that we support. Follow the workflow in
the petsurfer documentation is you want assistance.
On 6/21/2022 4:40 AM, Bouchra Guelib wrote:
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Hi,
I want to register PET to T1 MRI
. Juni 2022 um 16:36 Uhr schrieb Douglas N. Greve
:
*Caution: External email*
Sorry, I thought I sent an email responding to this. Try running
it with -run-wise. This will analyze each run separately. I can't
remember whether it generates a final combined average (been a
long
I'm not sure that will work. You should use mri_sclimbic_seg
https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic
On 6/27/2022 3:31 AM, Mostafa Fakhri wrote:
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Hello to all of you
I ran recon-all:
$ recon-all -sd /share/users/mfakhri/FS/subjects -subject
-all.log file
thnx.
*보낸 사람:* Douglas N. Greve 대신
freesurfer-boun...@nmr.mgh.harvard.edu
*보낸 날짜:* 2022년 6월 24일 금요일 오후 11:31
*받는 사람:* freesurfer@nmr.mgh.harvard.edu
*제목:* Re: [Freesurfer] ERROR : mri_ca_register with non
Sorry, I thought I sent an email responding to this. Try running it with
-run-wise. This will analyze each run separately. I can't remember
whether it generates a final combined average (been a long time since I
used this option), but run it and see what it does.
On 6/23/2022 2:00 PM, Caspar
Can you send the recon-all.log file?
On 6/21/2022 6:44 AM, 김다운 wrote:
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Hello FreeSurfer Develops,
I'm attempting to run recon-all on two single subject with T1.
However, I got the following error message for subject respectively:
256 256 256
Would tell me where is my mistakes
Le dim. 19 juin 2022 à 22:43, Douglas N. Greve
a écrit :
You can try removing --default-seg-merge, but it may fail.
It can compute a relative SUV (relative to a give n ROI). By
default, this will be pons, but you can chose others. SUV
On 6/20/2022 3:42 PM, Julian Macoveanu wrote:
> External Email - Use Caution
>
> Dear Freesurfers,
>
> I have a simple design with patients and controls and would like to
> find regions showing group differences in cortical volume and
> thickness. I also remove the effect of age, sex
:* freesurfer-boun...@nmr.mgh.harvard.edu
im Auftrag von Douglas N.
Greve
*Gesendet:* Sonntag, 19. Juni 2022 16:58:18
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] Problem with longitudinal processing
When you say they are growing rather than shrinking, do you mean in
the longitudnial
the strange figure with this email.
Thank you for answering my previous questions and looking forward to
your reply.
Thanks in advanced,
Yu
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Date: *Sunday, June 19, 2022 at 9:50 AM
*To: *freesurfer
of the files like for instance the
T1.mgz do to differences in the normalizations.
On Sun, Jun 19, 2022, 3:55 PM Douglas N. Greve
wrote:
You should be able to run 7.2 on top of the 5.3 and at will take
all your edits (make a copy of your 5.3 data first:)
On 6/14/2022 5:26 PM, Aaron
A postdoctoral fellow position in the Lab for Computational Neuroimaging
(LCN) under Dr. Douglas Greve is available. We are seeking a highly
motivated and talented researcher to pursue independent research. The
role will be to develop new algorithms within FreeSurfer, including
multi-modal,
but it doesn't work
PS: does mri_gtmpvc compute SUV? or the mean intensity?
Le dim. 19 juin 2022 à 20:55, Douglas N. Greve
a écrit :
what is your mri_gtmpvc command line?
On 6/19/2022 2:22 PM, Bouchra Guelib wrote:
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These are the missing regions
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