On 11/29/2021 11:55 AM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
A quick question.
Is it feasible or even possible to edit the aseg.mgz using another
program (i.e. ITK-snap after converting to nifti), and rerunning the
pipeline using the revised aseg as input
In your mkanalysis command, why are you specifying the mask and the
funcstem? These are tricky options to get right ...
On 11/29/2021 9:50 AM, Hiersche, Kelly J. wrote:
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Hello FreeSurfer Developers,
First, I am new to using Freesurfer, so I apologize if
Right. Actually, I don't think it would apply the smoothing to the
annotation anyway
On 11/29/2021 10:43 AM, Daniel Westfall wrote:
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Good afternoon,
It is my understanding that if I am only interested in the already
averaged region ROIs that are output
in a different format.
Thanks,
Nilab
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* 29 November 2021 04:01
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Help
Can you send some
sorry, no picture attached. Can you resend?
On 11/29/2021 2:40 AM, achille.teil...@chu-lyon.fr wrote:
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Dear experts,
We are working with a large MRI dataset (FLAIR, T1) and we are
performing recon-all based on the 3D T1. At the end, no error is
detected
If they are not part of the T1w series, then you can delete them (but
then they should not have caused the error). If they are part of the
series, then they are probably corrupted or perhaps the output of a very
aggressive anonymization.
On 11/25/2021 8:40 AM, Alison McDonnell wrote:
st,
AJ
Scanners used for controls and test subjects:
Achieva_TFE_R1
Achieva_TFE_R2
Ingenia_R1
Ingenia_R2
GE_SPGR_1529_R1
GE_SPGR_1529_R2
GE_SPGR_R1
GE_SPGR_R2
Phillip_Achieva_R1
Achieva_R2
GE_R1
GE_R2
On Sun, Nov 28, 2021, 20:41 Douglas N. Greve
wrote:
Also samseg, see *MailS
This is a bug. I've put a new version of mri_annotation2label here:
https://gate.nmr.mgh.harvard.edu/safelinks/greve/
username 'guest'
password 'collab'
copy it into $FREESUFER/bin (after making a copy of the one that is there).
On 11/22/2021 12:23 PM, Dr. Cornelius Kronlage wrote:
>
That will work; it may be clearer to use mris_fwhm, eg,
mris_fwhm --smooth-only --s sub-0006 --hemi lh --fwhm 5 --cortex --i
input --o output
On 11/26/2021 6:48 AM, Mason Wells wrote:
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Hi Experts,
This question may have been addressed elsewhereon the
For volumes, load labels using the "Load ROI..." under the File menu
For surfaces, use the "Load" button in the "Label" section
On 11/23/2021 2:44 PM, Shapiro, Noah Lorenz wrote:
Hello,
I am very new to FreeSurfer, and I was going through the tutorials and
bumped into difficulties when
Just add -cw256 to the recon-all command line
On 11/23/2021 8:34 AM, Alison McDonnell wrote:
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Hi Tim,
I looked at orig.mgz and it seemed fine and could see the whole head.
i dont know what is meant by the flag -cw256 error. I am taking over a
project
Can you send some pictures?
On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:
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Hi,
I am editing subjects for a research project. After reconstruction,
some parts of the brain are not included in the segmentation. Often,
some parts of the temporal lobe and
Yes, but if there is an anat2orig2diff.bbr.lta file, use that instead
On 11/22/2021 12:48 PM, Zeng, Qi wrote:
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Sorry for the trouble, I seemed to find the registration matrix
located in xfms/anatorig2diff.bbr.dat. Is that one correct?
Best,
Jackie
On
I noticed that you are explicitly setting the mask and funcstem in
mkanalysis-sess. Is there a reason for that? Also, I'd set -poly to 5.
On 11/21/2021 1:11 PM, Hiersche, Kelly J. wrote:
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Hello FreeSurfer Developers,
First, I am new to using Freesurfer,
I see what you mean, though I don't think either one look that great.
The first thing to do is to backup and look at the registration to
fsaverage_sym by mapping the lh and rh curv to lh.fsaverage_sym and see
if the curv patterns match up with those in fsaverage_sym and to each
other (use
That is a label atlas; you cannot run that through FS. You will need a
t1-weighted image to use as input to recon-all to start.
On 11/19/2021 1:59 PM, Flanagan, Shawn D wrote:
External Email - Use Caution
Hello,
I would like to use the Brainnectome atlas for cortical thickness
Also samseg, see https://pubmed.ncbi.nlm.nih.gov/33940143/
On 11/26/2021 11:16 AM, Fischl, Bruce wrote:
Hi AJ
you might try SynthSeg, as that is one of the advantages of it - it
isn't biased towards any particular MRI sequence
cheers
Bruce
Hi Christine, yes, your interpretation is correct. The -3T flag only
applied when using the mni tools, so it has no effect with ANTS. What
was the nature of the failure? We might be able to tweak the ANTS
command line to improve it.
doug
On 11/15/2021 12:52 PM, Notestine, Christine wrote:
it is not clear why it failed. Can you look at nu.mgz to see if
anything looks weird about it?
On 11/18/2021 1:43 AM, Wei Shao wrote:
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Hi, Dear Freesurfer experts
I'm have met a recon-all errors with data collected recently like this
They are mni305 coordinates
On 11/19/2021 9:41 AM, Gonzalo Rojas Costa wrote:
> External Email - Use Caution
>
> Hi:
>
> "Vertex Talairach" in tksurfer: how does it relate to MNI coordinates?
>
> Sincerely,
>
>
> Gonzalo Rojas Costa
> Department of Radiology
> Clínica las Condes
have you looked at this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 11/19/2021 9:15 AM, Gonzalo Rojas Costa wrote:
> External Email - Use Caution
>
> Hi:
>
>I have MNI 152 coordinates equivalent to 10-10 and 10-20 EEG
> electrodes (see Supplementary Tables 1
don't know. try figuring out which step is actually changing
On 11/18/2021 2:03 PM, Brusaferri, Ludovica wrote:
Hi!
I am using a pipeline that was implemented and validated using fs 5.3 , which
does the following:
* compute transformation matrix for linear registration of SUV with T1-2mm,
For those interested in PET and BIDS, this should be pretty useful.
Forwarded Message
Subject:OpenNeuroPET hackathon at MGH -- Dec 6th and 7th
Date: Wed, 17 Nov 2021 19:31:48 -0500
From: Wighton, Paul
To: Greve, Douglas N.,Ph.D.
Hi Doug,
I was hoping you
: Option T2.reg
is unknown"
*Gesendet:* Mittwoch, 17. November 2021 um 16:11 Uhr
*Von:* "Douglas N. Greve"
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] Using Mri_vol2surf
Can you be more specific about why it is not working? You definitely
need to run bbregister to cre
wow, that is weird. The RH extends far into the LH. What does the
aseg.presurf.mgz look like? Are the cortices and WM properly separated
left-right?
On 11/15/2021 4:33 AM, Alec Süwolto wrote:
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Hello freesurfers,
I’m new to freesurfer and I can’t fix a
You need to tell it what to do, eg, -all to do everything.
On 11/15/2021 8:49 AM, Alison McDonnell wrote:
External Email - Use Caution
recon-all.log is attached. have tried to run again with different data
and had the same problem
On Wed, 10 Nov 2021 at 22:39, Douglas N. Greve
You have 16 groups so you need 16 items in the contrast vector (assuming
no continuous variables), so you need something like
-1 +1 repeated 8 times to give you 16
On 11/17/2021 7:23 AM, Thalhammer, Melissa wrote:
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Dear Freesurfers,
I am struggling with
Can you be more specific about why it is not working? You definitely
need to run bbregister to create a registration file
On 11/17/2021 7:09 AM, m-maiw...@web.de wrote:
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Dear List,
I first run the recon-all stream using a MPRAGE as input, then
bbregister
Does that file exist? Have you manually/visually checked that subject?
Probably recon-all just did not finish
On 11/17/2021 12:13 AM, a Chinese reader wrote:
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Dear Freesurfer experts,
When I run the command "recon-all -s <> -qcache" ,
ERROR: cannot find
I'm not sure what is happening. Does it work without the parallel flag?
btw, you are not using 7.2
here's your build: build-stamp.txt:
freesurfer-linux-ubuntu18_x86_64-dev-20210824-e101185
On 11/16/2021 4:26 PM, Peled, Noam wrote:
Dear Freesurfer group,
I was running recon-all (Freesurfer
to
FS 6.
Best,
El vie., 12 nov. 2021 15:51, Douglas N. Greve
escribió:
If you are going from 5.3 to 6, you should just be able to run
recon-all -all on the 5.3 folder and it should take into account
your previous edits (make a copy first though:)
On 11/12/2021 4:40 AM, Steve
Have you seen this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 11/12/2021 6:23 AM, Alberto Del Cerro Leon wrote:
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Hello Freesurfer team, I did a white matter atlas from surface annot
with mri_aparc2aseg. However, when I use
If you are going from 5.3 to 6, you should just be able to run recon-all
-all on the 5.3 folder and it should take into account your previous
edits (make a copy first though:)
On 11/12/2021 4:40 AM, Steve Petersen wrote:
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Dear all,
We conducted the
On 11/12/2021 3:29 AM, Alice Giubergia wrote:
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Thanks for your replies Doug! I copied the previous messages below,
since I did not menage to retrieve the original email.
1) Thanks.
2) Regarding question number 2, yes that was what I meant.
3) I ran the
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, November 11, 2021 5:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] permutation simulation errror
What do you get if you run
stem2fname /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitle
Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, November 11, 2021 3:46 PM
*To:* freesurfer
Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, November 11, 2021 3:05 PM
*To:* freesurfer
Qi
On Thu, Nov 11, 2021 at 3:28 PM Douglas N. Greve
wrote:
For the DOSS case, yes.
On 11/11/2021 3:23 PM, Zeng, Qi wrote:
External Email - Use Caution
Hi Douglas,
If to set up the FSGD as below, is my design matrix for case and
control comparison as "1
on behalf of Douglas N. Greve
*Sent:* Thursday, November 11, 2021 2:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] permutation simulation errror
That is for mri_glmfit, not mri_glmfit-sim.
On 11/11/2021 3:24 PM, Brown, Alexander wrote:
External Email - Use Caution
Francke Drive
Columbia, MO 65211
Contact: 573-884-8779
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, November 11, 2021 2:04 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject
ite 81.3 1558515.86
Best,
Qi
On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve
wrote:
I would advice setting up the FSGD files with 8 classes based on
your 3 discrete, 2-level variables, eg, MaleControlWhite then use
two continuous variables Age and eTIV.
You should definitely
nombre de Douglas N. Greve
*Enviado:* miércoles, 10 de noviembre de 2021 15:09
*Para:* freesurfer@nmr.mgh.harvard.edu
*Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
Ah, I see. Can you upload those two subjects using the method below?
From the linux command line,
Create
uot;White"1187649.47
or 3)
Variables AgeGenderRaceeTIV
InputSub001_base"Control"85"Female""White"1350519.71
InputSub002_base"Control"81.3 "Male""White"1558515.86
InputSub003_base"Control"72.7 "Male""White"
...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Wednesday, November 10, 2021 4:40 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] permutation simulation errror
WARNING: This message has originated from an External Source. This may
be a phishing expedition that can result
sorry, can you include the previous emails in this thread along with
your new questions?
On 11/11/2021 11:44 AM, Alice Giubergia wrote:
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Thanks for your replies Doug!
1) Thanks.
2) Regarding question number 2, yes that was what I meant.
3) I ran the task
You cannot use flair as the main input. It has to be t1w; you can only
use flair as an additional input to help fix the pial surface
On 11/11/2021 2:30 PM, Devarajan, Alex wrote:
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Hello,
I'm running a fairly large database of MRIs through freesurfer for a
You can create a "patch" with something like
label2patch -surf white fsaverage lh lh.V1_exvivo.label ./lh.patch
then load it with
tksurferfv fsaverage lh white -patch ./lh.patch
When you load a patch, you will only be able to see the patch of the
surface that you loaded it on
If you want to be
rror: Input line 1, subjid = sub001_base
Variable 2 has character string Female
Variables should be continuous numbers
FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input
Also attached FSGD file below.
Thank you so much for the help!
Best,
Zeng
On Wed, Nov 10, 2021 at 5:41 PM Douglas N. G
please send your command line and full terminal output as well as the
fsgd file
On 11/10/2021 5:12 PM, Zeng, Qi wrote:
External Email - Use Caution
Hi Freesurfer experts,
Here, I want to design a simple group comparison (two levels: Case vs.
Control) and also count for 4 covariates
Which version of FS are you using? Can you send the log file created by
mri_glmfit-sim (different than the one you sent)?
On 11/10/2021 3:49 PM, Brown, Alexander wrote:
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Hello,
I am attempting to run a permutation simulation to correct for
multiple
And send the recon-all.log file
On 11/10/2021 10:57 AM, Alison McDonnell wrote:
External Email - Use Caution
the full line after setting up the environment is
recon-all -i /Users/ali?Arch_Raim/IM-0001-0001.dcm -s IM-0001 -all
On Wed, 10 Nov 2021 at 15:53, Tim Schäfer
On 11/10/2021 9:48 AM, Alice Giubergia wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I'm interested in performing a functional analysis on task-based data.
I was taking as an example the
"FsFastFunctionalConnectivityWalkthrough" tutorial but, if I got it
correctly,
e spam.
Many thanks,
Gonzalo.
*De:* freesurfer-boun...@nmr.mgh.harvard.edu
en nombre de Douglas N. Greve
*Enviado:* martes, 9 de noviembre de 2021 20:13
*Para:* freesurfer@nmr.mgh.harvard.edu
*Asunto:* Re: [Freesurfer]
It will be safest if you use the same command (in the sense that all the
files will be up-to-date). If the surfaces are ok and you really don't
want to regenerate them, then I think you can just use
recon-all -s subject -aparc2aseg -segstats
There may be some operations that will see that the
?
*De:* freesurfer-boun...@nmr.mgh.harvard.edu
en nombre de Douglas N. Greve
*Enviado:* martes, 9 de noviembre de 2021 18:09
*Para:* freesurfer@nmr.mgh.harvard.edu
*Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2
They are done simultaneously
On 11/9/2021 11:38 AM, Turnbull, Adam wrote:
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Hello,
I just wanted to confirm whether Freesurfer performs temporal
filtering simultaneously with nuisance regression, or whether it
performs these steps subsequently in either
a gifti image with 10242 vertices and 475 time
points. The following is the information:
Screenshot 2021-11-09 at 16.47.58.png
Do I need to transfer the images to you?
On Tue, 9 Nov 2021 at 16:26, Douglas N. Greve
wrote:
I have a feeling that it may be ignoring the extra frames
-boun...@nmr.mgh.harvard.edu
en nombre de Douglas N. Greve
*Enviado:* martes, 9 de noviembre de 2021 14:49
*Para:* freesurfer@nmr.mgh.harvard.edu
*Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
⚠ Caution: External sender
The white surface won't change, but the pial surface
smoothing output with n = 2
Saving target data
Saving to
/Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
Best,
Yangwen
On Tue, 9 Nov 2021 at 15:49, Douglas N. Greve
wrote
The white surface won't change, but the pial surface should change. Can
you verify that the pial surface changed?
On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:
External Email - Use Caution
Hello,
I wanted to compare the results of the aparc.stats on the same
subjects when only
please send your command line and terminal output
On 11/9/2021 6:05 AM, Yangwen Xu wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I am trying to smooth images using mri_surf2surf. Here is the command
line:
'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval
You could run it up to the skull stripping (-autorecon1), then compute
the brain volume yourself from the skull-stripped image. You could also
use samseg; samseg only takes an hour or so to run and outputs a measure
of total intracranial volume, but you could also extract total brain
volume
On 10/29/2021 10:46 AM, Kang, Jee Won wrote:
External Email - Use Caution
Hello all,
There are two topics I would appreciate your expert advice on:
Topic 1: Aseg and wm edits
I was going through the wiki and the archive of past inquiries and was
unable to find a clear answer
On 10/27/2021 11:39 AM, Douglas N. Greve wrote:
Dealing with discrete variables as discrete is the way I would do it
as you would not have any reason to think that there is some linear
relationship between your the (arbitrary) values you assign to
discrete variables and thickness. Age
On 10/29/2021 10:39 PM, Zeng, Qi wrote:
External Email - Use Caution
Hi Experts,
After completing long_mris_slopes to get the rate of change and then
concatenating them into one.mgh file for group analysis
(mris_preproc). I am finally getting to mris_glmfit. Got a couple of
You can use tksurferfv (this is a frontend for freeview that takes most
of the original tksurfer options)
On 11/3/2021 1:11 PM, Fischl, Bruce wrote:
Hi Arian
Tksurfer has been deprecated for a long time. Can you try freeview
instead?
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
/
/McGill University
/
/Montreal Neurological Institute/
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Wednesday, November 3, 2021 11:08 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject
So you want to map the labels in fsaverage into MNI152 volumes pace,
right? After mris_divide_parcellation, you should have a parcellation in
fsaverage space. Use mri_surf2surf (or mris_apply_reg) to map that into
the MNI152 that you ran recon-all on. Look in the recon-all.log file for
the
Did you see this response from a few days ago?
On 10/27/2021 11:26 AM, Douglas N. Greve wrote:
I'm not sure what you did or how to interpret that pic. If I
understand, you ran a case through recon-all and created labels on
that case. You then recon-all again using a totally different output
There is nothing special you have to do. What version of FS do you have?
You still have to source the FS environment. If you can run recon-all,
you should be able to run PETsurfer
On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote:
Hi!
I have been using freesurfer regularly and I am now
To add on to that, dt_recon will register you DTI to the FreeSurfer
anatomical analysis. It will on generate FA, diffusivity, etc. I don't
know how to get that interfaced with output from MRtrix3
On 10/29/2021 5:09 PM, Mora, Jocelyn S. wrote:
Hi Reshma,
Yes, you would use the FreeSurfer
That is what I would do. The FS WM volumes are computed using the
surface, so it will be more accurate (and probably a little bigger)
On 10/29/2021 3:59 AM, Nederpelt, D.R. van (David) wrote:
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External Email - Use Caution
Dear SAMSEG developers,
You did not send your recon-all command but my guess is that it stopped
without error because you did not include a directive (eg, -all). But in
any event, you cannot run an MT image through recon-all
On 10/29/2021 3:35 AM, Marlene Tahedl wrote:
> External Email - Use Caution
>
> Hi!
>
There are answers embedded in your email
On 10/27/2021 12:36 PM, Billah, Tashrif wrote:
Thank you Douglas, I enjoyed reading your referral. However, I did not
get answer to any of my questions. Can you take a second look?
Best,
Tashrif
Date: Wed, 27 Oct 2021 11:41:35 -0400
From: "Doug
not sure what you mean by "manual segmentation" or why you would do that
again. We do recommend at least inspecting the data visually
On 10/27/2021 11:35 AM, 刘卫 wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I would like to ask, on free surfer, can I directly
On 10/27/2021 10:58 AM, Billah, Tashrif wrote:
Hi,
1. What is the name of the space of wmparc.mgz? I see that it is in
the same space of brain.mgz.
Yes
1.
2. What transform file brings orig/001.mgz to brain.mgz?
See https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Dealing with discrete variables as discrete is the way I would do it as
you would not have any reason to think that there is some linear
relationship between your the (arbitrary) values you assign to discrete
variables and thickness. Age is not an arbitrary value, so I would use
that as a
We have not used COR format in years. Why do you need it?
On 10/26/2021 3:17 PM, Alireza Karami wrote:
External Email - Use Caution
Hello
I used the following command to create the surface of my subject:
recon-all -s subj -i anat.nii -all -qcache -3T
However, some files are missing
I don't think there is anything specific for the --table option, but
everything else is the same.
On 10/24/2021 4:31 PM, Alvarado,Luis R wrote:
External Email - Use Caution
Hi Douglas,
I was wondering if there are any “--table option” specific tutorial
for the mri_glmfit function.
I'm not sure what you did or how to interpret that pic. If I understand,
you ran a case through recon-all and created labels on that case. You
then recon-all again using a totally different output where you improved
the homogeneity. You now want to map the labels you created on the 1st
run to
Do you have proper permissions for it?
On 10/22/2021 8:48 AM, g.ton...@libero.it wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
Thank you for your work !
I am trying to segment .nii images with FS, using an ubuntu shell in
Windows 10. When I run the command
On 10/21/2021 6:59 AM, Wacker, Ewa Helene wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
for my project I am using Freesurfer 7.1 to examine the hippocampal
volumes of patients with major depressive disorder (and controls)
using the automatic segmentation.
What platform are you using?
On 10/20/2021 11:02 AM, DIANA ORTEGA CRUZ wrote:
External Email - Use Caution
Dear FreeSurfer team,
I am experiencing a display problem in the FreeView version of
FreeSurfer 7 for inflated surfaces. The inflated surfaces from my
fsaverage folder look as
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, October 18, 2021 9:52 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Local GI MRI_segstats error
please send your command line and terminal outout
On 10/11
Not easily. You would have to find a way to map the AAL into the
individual subject's space. Then you can just specify that volume and
the desired index when running fcseed-config
On 10/19/2021 3:24 AM, std...@virgilio.it wrote:
External Email - Use Caution
Hi
is possible to use
have you double checked the orientation of the data in freeview? Eg, is
the axial view in freeview truly showing you the axial view of the brain?
On 10/18/2021 11:39 AM, Sarkis, Rani A.,M.D.,M.SC. wrote:
Hello all,
I have an issue with a study, and am wondering whether it can be fixed.
You might have introduced a new defect, or just made an existing one
worse. If there are topo defects, you can't just ignore them. You don't
necessarily have to remove all the dura. Typically there is a
"peninsula" where the main WM attaches to the the "island" of dura. All
you have to do is
I'm not sure what a ribbon for the inflated surface would look like. You
can try mri_surfacemask to create a binary volume of everything inside
the surface.
On 10/14/2021 7:47 PM, Nicolas Munera Garzon wrote:
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Greetings freesurfuer community,
I've been
Not really. If you pass it an input that is already ACPC, you can add
-conform-dc to keep the orientation.
On 10/14/2021 9:44 AM, Zhengchen Cai wrote:
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Hello FreeSurfer Developers,
I wonder if we have a function that could automatically align T1w to
it will inevitably create systematic differences
On 10/14/2021 8:40 AM, Castro Leal, Gonzalo wrote:
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Dear Freesurfer,
I was wonderign wether processing scans and comparing their stats,
e.g. cortical thickness and
Can you send your command line, terminal output, and a list of the files
that it did create?
On 10/13/2021 4:33 PM, Jingyi Wang wrote:
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Dear Freesurfer experts,
I am trying to obtain parahippocampus segmentations from the
"?h.aparc.a2009s.annot" file.
please send your command line and terminal outout
On 10/11/2021 1:36 PM, COLLEEN PLETCHER wrote:
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Hello,
I am trying to run mri_segstats for local GI indices. I am getting a
file not found error for
/tmp/mri_segstats.tmp.sub-1007_ses_01/.lh.176.ctab
I
You can also run recon-all on the mni152, then run. Load it with your
volume-based atlas to make sure that the alignment is good and that the
surfaces surround your labels, then run
mri_vol2surf (--projfrac 0.5) on your volume-based atlas to create a
surface-based atlas, then run mris_seg2annot
I don't know what you are asking. Can you elaborate? It is helpful to
indclude commanb lines to show how files were created
On 10/9/2021 1:30 AM, Dongyue Zhou wrote:
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Dear FreeSurfer experts:
I use the 'qcache' command to get the file
mask is not being changed
from the control points, which volumes do you suggest we use to see
white matter changes after multiple edits?
Thanks
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
I don't know what you mean. Can you elaborate?
On 10/8/2021 5:27 PM, Zeng, Qi wrote:
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Hi Experts,
If I want to analyze and visualize baseline and follow-up for an
individual subject's change (before-after & after-before). Should I
treat it as a
On 10/8/2021 8:51 PM, Dongyue Zhou wrote:
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Dear FreeSurfer experts:
I want to know cortical thickness in this file
'subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh' is in standard
space or in native space.
standard
Is not the common coordinate
2021 19:52, Annalisa Lella ha scritto:
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Pre-processed with recon all
Il 8 ott 2021 19:50, "Douglas N. Greve"
ha scritto:
What do you mean by "elaborated"?
On 10/8/2021 1:29 PM,
in freeview, and verify
that it is in the correct location.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Friday, October 8, 2021 10:49 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re
If you have not done manual editing, then just rerun in 7.2 from scratch
On 10/8/2021 1:52 PM, Annalisa Lella wrote:
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Pre-processed with recon all
Il 8 ott 2021 19:50, "Douglas N. Greve" ha
scritto:
W
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