anks again for all your assistance.
~Erik Jahner
On 11 Jul 2021, at 7:52 AM, Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>> wrote:
On 7/10/2021 12:47 AM, Erik Jahner wrote:
External Email - Use Caution
I am interested in obtaining the average intensity within a lab
are on volumetric data parcellated using aseg and not
surface data.
Does mri_glmfit work with the output of the asegstats2table or on
voxelwise FA maps ?
Many thanks
Rito
On Fri, Jul 9, 2021 at 4:04 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
On 7/9/2021 11:44 AM, Rit
for eTiV
or total surface area?
Thank you so much,
Elisabetta
Sent from my iPhone
On Jul 9, 2021, at 2:08 PM, Douglas N. Greve
wrote:
I'm not sure what you mean. Can you elaborate?
On 6/30/2021 5:05 PM, Del Re, Elisabetta wrote:
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External Email
On 7/10/2021 12:47 AM, Erik Jahner wrote:
> External Email - Use Caution
>
> I am interested in obtaining the average intensity within a label from each
> frame of a functional image that has been smoothed on the surface (I have
> generated the label). However, the functional
On 7/9/2021 11:44 AM, Ritobrato Datta wrote:
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Hi All,
I have the following data –
I have 205 subjects - each subject was imaged at 3 timepoints
(baseline, followup 1 and followup 2)
The 205 subjects are split in two treatment arms with 100 subjects
Try running it without the -parallel flag. If you want to use multiple
cores, then add -threads N (N= number of cores)
On 7/6/2021 4:29 AM, Susanne Gellißen wrote:
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Dear FreeSurfer Developers,
I am processing MRI data using the freesurfer processing stream
In FreeView, go to "View/Edit". From the resulting interface, you can
turn on and off any parcellations you want.
On 7/5/2021 1:04 PM, Ellen Ji wrote:
> External Email - Use Caution
>
> Dear experts,
>
> I have a basic visualization question.
> I would like to create a surface brain
We refer to this operation as "conforming".
This page might help
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 7/4/2021 4:39 PM, Alexander Rockhill wrote:
> External Email - Use Caution
>
> Hello,
>
> I am trying to replicate the processing steps that occur
By my count, you entered 36 weights. I'm not sure why it says you only
entered 1, but try the correct number of weights first and see if the
problem goes away
On 7/3/2021 2:08 PM, Marilena Wilding wrote:
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Dear
ROI-wise and vertex-wise analyses are different and may give different
results. The vertex-wise analysis looks at individual vertices whereas
ROI-wise averages over all the vertices. It is possible (even expected)
that averaging over all vertices will reduce the variation and give
stronger
You can use the reposition surface tool in freeview. Just be careful
that you don't overwrite it if you re-run
On 7/2/2021 3:37 AM, Rosalia Dacosta Aguayo wrote:
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Dear Freesurfer's experts,
I wonder if there is any chance to correct the pial surface when
which results? sig maps (and other maps) are surface overlays. You can
convert them to nifit format, but they will still be surface overlays
(so you would not view/analyze them in FSL or SPM)
On 7/1/2021 9:12 PM, Sonya Gupta wrote:
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Hi,
Hope you are
That does not apply to the recon-all command, only to
mri_segment_hypothalamus_subunits
On 7/1/2021 12:23 PM, g.ton...@libero.it wrote:
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Hello FreeSurfer Developers,
Thank you for your work !
I successfully set up Freesurfer and ran a test on my
you should not pass it a label. If you look at the help,
Functional ROI-based options
-roi fcconfig : as created by funcroi-confg
On 7/1/2021 10:58 AM, Nasiriavanaki, Zahra wrote:
Hello Freesurferers,
I’m trying to use a functional label (extracted from task functional
BOLD data), as a
There should be a file called something like gamma.table.dat
This is a text file with the differences for each ROI and contrast.
On 7/1/2021 4:39 AM, Thalhammer, Melissa wrote:
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Dear FS experts,
I have run mris_preproc and mri_glmfit for group analysis as
comparing groups.
Thank you for your advise,
best wishes,
Elisabetta
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Sunday, June 20, 2021 10:34 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] LGI FS 7.1
The biggest changes are intensity
You cannot use a DODS in this design as it tries to fit an offset and a
slope for each class, which can't be done when the class has only one
member. Try using DOSS instead. You should probably demean and rescale
the eTIV to be between 0 and 1.
On 6/29/2021 11:19 AM, Dr. Cornelius Kronlage
On 6/29/2021 3:32 AM, Rosalia Dacosta Aguayo wrote:
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Dear Freesurfer team,
I am inspecting the different participants I have run recon-all -all
and I have found different errors I would like to discuss with you
before proceeding as I am new with this
Douglas
please find the terminal output and the log files attached.
when I run this command in FS 6.0.0, no error occurred
thanks in advance
cheers
Jürgen
Am 27.06.2021 um 16:49 schrieb Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>:
Can you send the mri_glmfit.log file fro
Generally, you do not smooth it as averaging over the ROI is effectively
a type of smoothing. If you were to smooth prior to the averaging, you'd
get one area smearing into another.
On 6/28/2021 12:57 PM, Ryan Bell, Ph.D. wrote:
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Dear Freesurfer Experts,
try $FREESURFER_HOME//matlab/annotval2surfoverlay.m
On 6/25/2021 2:55 PM, Fischl, Bruce wrote:
I guess doing it in matlab would be easiest
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Hye Min Shin
*Sent:* Friday, June 25, 2021 1:24 PM
*To:* freesurfer@nmr.mgh.harvard.edu
We generally do not normalize it by anything. ICV norm is not needed
because thickness does not scale with head size. Sometimes people will
normalize by mean thickness, but that changes the question being
answered, so that is more a question for you
On 6/24/2021 3:01 PM, Gabbo Ramírez García
Can you send the mri_glmfit.log file from your mri_glmfit run?
Can you run mri_glmfit-sim with --debug as the first option and capture
and send the output?
On 6/23/2021 4:42 AM, juergen.haen...@upd.unibe.ch wrote:
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Dear FS experts
I have run stats using
No, it should not
On 6/22/2021 4:12 PM, miracle ozzoude wrote:
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Hello All,
I was wondering if the Right/Left-Cerebral-White-Matter in the
aparc+aseg.mgz contains WM hypointensities.
mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats
sorry for the delay, Yes, the eTIV is in the aseg.stats file
On 6/22/2021 2:57 PM, Gallego Angel, Juan wrote:
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Hello,
I sent the message below a couple of weeks ago but I haven’t seen it
posted in my freesurfer digest emails. I am wondering if I need to
First, try using tksurferfv (this is the freeview version of tksurfer;
tksurfer is obsolete)
Second, you'll have to tell us more than "it did not work" (eg, send the
terminal output or some other description)
On 6/21/2021 3:03 PM, Lab of Autism and Developmental Neuroscience, Lab
of Autism
On 6/21/2021 12:13 PM, Yu-Wei Chang wrote:
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Dear PetSurfer and Freesurfer Developers,
I would like to run partial volume corrections on amyloid PET images
(from ADNI) with PetSurfer.
I have downloaded the amyloid
Can you get the data to us? You can follow these instructions
From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use
discuss it further with
the engineers as we are at the very beggining of the acquisition.
Kind regards,
Rosie
El jue., 24 jun. 2021 17:10, Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>> escribió:
It looks like the data are fairly low quality. This will require
some manual int
it should not have hypointensities (as long as they are labeled as such)
On 6/24/2021 12:07 PM, miracle ozzoude wrote:
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Hello,
I was wondering if anyone has an answer to my question.
Cheers
On Wed, Jun 23, 2021 at 5:42 PM miracle ozzoude
In Freeview, hit the "View/Edit" button. The resulting interface will
allow you to hide/show any combination of labels. You can hit the "All"
button to turn them all off and then just add the ones you want.
On 6/24/2021 12:11 PM, Jennifer James, MD wrote:
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Can you send the recon-all.log file?
On 6/18/2021 10:54 AM, Soichi Hayashi wrote:
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Hello. I am having a problem running freesurfer on a HCP 7T data and I
am wondering if someone from this mail list could help me out.
I am trying to run freesurfer
1. You need to be careful here demeaning. When you set up a linear
model, you have two parameters: the intercept and the slope. Without
demeaning, the intercept is defined to be where the line intercepts the
y axis at x=0 (in this case age=0, birth). When you demean age, you do
the test at
Have you tried dcm2niix? It's pretty robust
On 6/17/2021 6:59 PM, Christopher Mcnorgan wrote:
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Hi all,
I’ve been provided with some data collected on a 1.5T GE scanner from
an old published study. The paper doesn’t
Try mri_coreg. You can run it with multiple cores with --threads N
On 6/17/2021 8:48 AM, Marina Fernández wrote:
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Dear experts,
I would like to co-register T2 to T1 robustly, both images have a
resolution of 0.65mm3.
Firstly, I tried bbregister with the
Is there a question that you have?
On 6/17/2021 7:45 AM, 1248742467 wrote:
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Hello, Fs
I am not familiar with the exact steps of sampling a pre-segment file
into the FSAVERAGE5 space. In other words, I am not very familiar with
the exact steps of the
Sorry, it is too hard to try to read your code to figure out what is
going on. Is is possible that you are passing surface data into the
volume (mni305) analysis?
On 6/16/2021 11:51 AM, Pedersen, Walker Scott wrote:
I am trying to use fsfast to analyze task-based functional data output
by
You can do it in two ways.
- First, you can just apply mri_segstats with the --annot option to get
the mean NODDI values using the ?h.aparc.stats file, then compute the LI
on the ROIs
- Second, you can compute the map of the LI values (just added this here
Don't use --grf with surfaces
On 6/15/2021 7:24 PM, Paul, Jhelum wrote:
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Hello,
I also have the same error. I have been looking into all the tutorials
available for Freesurfer v7 and trying to search why,
mri_glmfit-sim --glmdir
If you are going to compare the volume across subject, then it does need
to be corrected with eTIV
On 6/15/2021 8:06 AM, AJ wrote:
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Hi,
After running longitudinal processing and creating base and long runs,
When looking at volumes of various structures
It looks like the data are fairly low quality. This will require some
manual intervention (control points, fixing topologogical errors, etc).
See our wiki on manual interventions
On 6/15/2021 10:52 AM, Rosalia Dacosta Aguayo wrote:
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Here is what I am
My understanding is that you compute the ratio on the uncorrected images
because the ratio will be free from bias (part of the motivation for
doing it)
On 6/14/2021 1:23 PM, Marina Fernández wrote:
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Dear experts,
I would like to create myelin maps
Why do you want to find the correspondence? The tool was not made to be
used this way, though I understand it is a little confusing. You are
supposed to register both left and right of your subject to the left
fsaverage_sym and do your processing there. The only reason to go to the
right of
Do I understand correctly that you are running recon-all with EPI data?
If so, that will certainly not work.
On 6/11/2021 11:46 AM, Michael Datko wrote:
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Hello,
I have been collecting data on a 7T scanner, with functional EPI data
collected with 1.5mm
Did you source the freesurfer enviroment?
On 6/11/2021 4:28 AM, Juan Felipe Quinones Sanchez wrote:
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Dear Freesurfer team,
I am new to Freesurfer. I installed it on my WSL (ubuntu 18.04)
following the instructions at: *MailScanner has detected a
GrayVol is the volume (mm3) of the gray matter for that stucture
ThickAvg is the average thickenss (mm) for that structure
On 6/11/2021 3:59 AM, Koustav Chatterjee wrote:
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Dear Sir/Madam,
Could you please tell what does it mean by 'Gray volume' and 'avg
, how can I perform vertex
by vertex (surface) analysis of covariance between functional
connectivity data (FS-FAST) and cortical thickness, regressing out
the effect of groups?My mean concern is how buid the fsgd file.
Stefano
Great news, thank you, Doug! Best, aga On 8/3/11 5:02 PM,
The biggest changes are intensity normalization and highres support, but
many more changes. See the release notes
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
On 6/9/2021 10:17 AM, Del Re, Elisabetta wrote:
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External Email - Use Caution
Try demeaning and normalizing the covariates.
On 6/9/2021 9:09 AM, Lurie, Lucy wrote:
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Hello
I am trying to a whole brain analysis with one group and five
covariates. I am getting an error that the design matrix may
Yes, you use a "per-vertex map" (--pvr option to mri_glmfit). See,
example, this thread
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18790.html
On 6/3/2021 10:22 AM, std...@virgilio.it wrote:
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Hi,
how can I perform vertex by vertex
no, humans only. Though if you google around you might find someone who
has adapted it
On 6/4/2021 4:33 AM, 胡俊涛 wrote:
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Can I use Freesurfer to process MRI image data of mice?
Thank you!
___
Freesurfer
Can you try an experiment for me?
cd $SUBJECTS_DIR/subject/surf
cp lh.sphere.reg lh.sphere.reg.auto # make a backup
mris_register -norot -rotate 0 0 +15 -curv rh.sphere
$FREESURFER_HOME/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
rh.sphere.reg
Then run
recon-all -s subject
On Tue, 1 Jun 2021 at 17:44, Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>> wrote:
There are not results to visualize, there is just a table. There
should be a sig table in the output folder
On 5/28/2021 9:37 AM, Aldinhas De Freitas Ferreira, Francisca wrote:
n
any form immediately.
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Douglas N. Greve
*Sent:* Thursday, May 27, 2021 6:13 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] recon-all errors
Can you check the registration of the FLAIR and T1?
cd subje
ly suggest
that something went wrong and I can trust the results?
Thanks.
On 6/1/2021 2:51 AM, Douglas N. Greve wrote:
The topology error labels might be be created if it did not finish.
YOu can try just loading the brain.mgz, the wm.mgz, and the
orig.nofix and see if you can find a big topo error
(unless you also add --no-tfe).
Best wishes,
Marina.
%%
Douglas N. Greve
<https://secure-web.cisco.com/1y-OD2P8BWHc0h287Xl8Diwwr6Ds9fMYa9s6RyGJbPbpYxPx3JIc0yXalZqJbTpbdASEaa25SaBP6BZrHh-ckK9p4KmnrShTPTQiliqNt53IQS-Nt9lXFyYjh1H-dvtew0E4TqUxoTOVFhv
liub wrote:
External Email - Use Caution
Thank you for your help !
I have run the command:
mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log
and got the nucor.log.
-原始邮件-
*发件人:*"Douglas N. Greve"
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log
and got the nucor.log.
-原始邮件-
*发件人:*"Douglas N. Greve"
*发送时间:*2021-06-01 08:35:38 (星期二)
*收件人:* freesurfer@nmr.mgh.harvard.edu
*抄送:*
*主题:* Re: [Freesurfer] Recon-all error :Segmentation fault (cor
look at the tutorial
On 6/1/2021 12:00 AM, Diógenes Bispo wrote:
External Email - Use Caution
I would like to know what other modification I should make to my
script to run --grf (volume analysis):
- mris_preproc ??
- mri_glmfit (--surf in white)
- mri_glmfit-sim ??
Thanks.
failed
I wonder is this means there is something wrong with the GLM I created
or if it is something wrong with my Freeview?
Thanks a lot in advance!
Kind regards,
Francisca
*From:* Douglas N. Greve
*Sent:* 27 May 2021 21:05
The topology error labels might be be created if it did not finish. YOu
can try just loading the brain.mgz, the wm.mgz, and the orig.nofix and
see if you can find a big topo error
On 5/31/2021 11:16 AM, Ellen Ji wrote:
External Email - Use Caution
Dear experts,
mris_fix_topology has been
On 5/30/2021 10:27 AM, Massieh Moayedi wrote:
External Email - Use Caution
External Email - Use Caution
Hi,
We’re collecting multiecho T1s. We have individual T1 images with
different echoes, and the RMS files.
I’ve run freesurfer using both the RMS files, and the multiple
The ces.nii.gz file will contain the percent with respect to the mean
signal in the brain.
The cespct.nii.gz will contain the percent with respect to the mean time
series of the voxel.
On 5/30/2021 9:42 AM, Star Xi wrote:
External Email - Use Caution
Hi, dear FS experts,
I'm
You can't use the --grf option with surfaces
On 5/29/2021 2:14 AM, Diógenes Bispo wrote:
External Email - Use Caution
Hi Freesurfer team.
I made the following command:
#!/bin/tcsh
setenv study $argv[1]
foreach hemi (lh rh)
foreach smoothing (10)
foreach meas (volume)
No, not easily. I think the field of view must be lower in that
dimension and so it is cropping.
On 5/28/2021 3:23 PM, Melissa Marie Rundle wrote:
External Email - Use Caution
Hi,
I am using mri_convert to change the orientation of an image in its
native space from LPS to PSR.
: [Freesurfer] WM or Pial edits to correct surfaces
Thanks Doug. Will try with difference distances. Where is the expert
file placed?
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf
How did you create the sig.mgh that you are trying to overlay?
On 5/28/2021 11:16 AM, Francisca Ferreira wrote:
External Email - Use Caution
Dear Experts,
I have extracted subcortical vols corrected for intracranial vols
using asegstats2table and I ran mri_glmfit using the
Yes, you can use PETsurfer. I would apply it to the ratio
On 5/28/2021 10:25 AM, Marina Fernández wrote:
External Email - Use Caution
Dear experts,
I want to calculate myelin maps using the ratio of T1w and T2w MRI
images. I saw that the correction of partial volume effects can be
of freesurfer.
Thanks,
Marianna
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* 27 May 2021 9:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Choosing projfrac/projdist
Not sure, can you try this
cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log
and send the file nucor.log
On 5/28/2021 7:51 AM, liub wrote:
External Email - Use
Try using tkregisterfv instead (it takes all the same command line args
but uses freeview
On 5/28/2021 2:13 AM, 张威 wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am attempting to manually register a cerebral blood flow images to a
T1 weighted images via the
There might be a couple things happening. First, I would try adding a
few control points in that area; make sure they are in true WM in voxels
that have a value less than 110 on the brain.mgz file. This might help
push the white surface further out (the WM in that gyrus is very thin).
It might
Can you check the registration of the FLAIR and T1?
cd subject/mri
tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta
--targ orig.mgz
On 5/20/2021 4:33 PM, Mark Wagshul wrote:
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Hi. I’m trying to run
You definitely do not want to use mni152.register.dat for this (I'm
surprised it even got close). Instead, register the orig.mgz to the
HCP842 template space, eg, with
mri_coreg --mov orig.mgz --targ HCP842.template.nii.gz --dof 12 --reg
reg.HCP842.lta
This will print out a tkregisterfv command
Try removing the trailing slash from the subject name, ie,
10100_S2654UFQ, not 10100_S2654UFQ/
On 5/26/2021 1:18 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
Hi all,
I am trying to extract LGI measures as prescribed in *MailScanner has
detected a possible fraud attempt from
you'll need to supply us with more information, eg, command lines and
why do you think it has the wrong dimensions
On 5/25/2021 11:53 PM, Mingyang Xia wrote:
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Dear freesurfer expert:
My name is Mingyang. I want to preprocess fmri image and map the
There is not one file for CSF or GM, but you can extract them from other
files. Eg,
mri_binarize --i aparc+aseg.mgz --ventricles --o ventricles.mgz
mri_binarize --i aparc+aseg.mgz --gm --o gm.mgz
You can use aparc+aseg.mgz as your brain mask
On 5/25/2021 6:14 PM, Camargo, Aldo wrote:
run it with -autorecon2 and -autorecon3
On 5/25/2021 1:47 PM, Camargo, Aldo wrote:
External Email - Use Caution
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Hi Bruce,
I was wondering if there is way to continue the process to recon-all
once I have done the recon-all with the option
If the tkregisterfv command works without the --surf option, then just
use that
On 5/18/2021 12:04 PM, Gabor Perlaki wrote:
External Email - Use Caution
Dear all,
I tried to check the talairach transformation under Freesurfer 7 linux
version
am asking.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, May 10, 2021 9:23 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mris_anatomical_stats
On 5/24/2021 12:32 PM, Francisca Ferreira wrote:
External Email - Use Caution
Dear Experts,
I am new to FS. I'm trying to run mri_glm fit
I've created FSGD with 2 classes -responders vs non-responders to a
given intervention- and 3 variables to be regressed out-according age,
No, not really
fov is field of view = voxelsize*number of voxels
frames are the number of frames in the file (ie, the 4th dimension)
dof = degrees of freedom we never use
xyz-start - edge of the volume
voxel to ras transform converts a column-row-slice into a
right-anterior-superior coordinate
Generally, control points are the way to go here. It looks like you have
put a bunch of them in cortex though
On 5/21/2021 12:14 PM, Kadwani, Manorama wrote:
Hi,
I am trying to correct the white matter segmentation in the second
image shown below. It doesn't include chunks of the temporal
If I understand you correctly, you have an ROI defined in the volume and
you want to transfer it to the surface. Is that right? First you should
look at the ROI in the volume along with the surfaces and make sure that
they pass through the ROI. I would generally use the projfrac-max option
for
I am looking at volume and fsaverage is(?) a
surface thing?
Haley
On Mon, May 10, 2021 at 11:15 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
It is saying that the mask
lhYeo2011_7NetworksConfidence_N1000.mgzdoes not have thee same
dimensions as the inpu
You could also run recon-all on the mni152 template, then run the
hippo/amyg seg on the output. It will give you the same bad segmentation:)
On 5/20/2021 9:21 AM, Iglesias Gonzalez, Juan E. wrote:
Hi Jessica,
There’s no direct way of doing this, since the atlas lives it its own
space and
This is more of a question for the PALM developer (whom I have cc'ed).
On 5/19/2021 8:15 AM, Marina Fernández wrote:
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Dear experts,
I used the function fspalm to run permutations with the following options:
fspalm --glmdir /my_glmdir/ --cft 1.3 --name palm
The easiest thing to do is to create a new stats file that has the same
basic format as the aseg.stats but with your desired measures in them.
Then specify the new stats file with --stats=newstatsfile when you run
long_stats_slopes
On 5/19/2021 1:06 AM, AJ wrote:
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Just create a text file (not bfloat) where each row is a different time
point. You can have multiple columns and can specify how many of them to
use in the analysis.
On 5/18/2021 5:03 PM, Eli Bulger wrote:
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Hello,
I am working with task-based functional
Are you sure those are the dimensions? They do not look right. It should
be something more like ~12x1x1x120
Try running
mri_info --dim fmcpr.up.sm5.self.lh.nii.gz
On 5/18/2021 1:26 PM, Mingyang Xia wrote:
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Dear freesurfer expert:
I am sorry to
I'm not sure what is going wrong with it, but you can do this yourself with
mri_binarize --i aparc+aseg.mgz --match 7 --o bin7.mgz
Then do the same with 8, 46, 47
On 5/17/2021 6:39 PM, A.R. Sekar wrote:
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Hello
On 5/17/2021 10:16 AM, Ellen JOOS wrote:
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Dear Freesurfer team,
I am currently preparing my first fMRI study and used OptSeq2 for
creating the trial sequence. Since I am not experienced with the study
design in MRI (I mainly conducted EEG studies so far), I would
It is possible. Try running defect-seg to see where the defects are. Run
it with --help to get more info
On 5/13/2021 2:20 PM, Dierker, Donna wrote:
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Hi freesurfer experts,
I have some cases where sulci near the
your tksurferfv command line is wrong
On 5/12/2021 6:06 AM, Bernardoni, Fabio wrote:
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>
> Dear Freesurfers
>
> I recently moved to FS7.1 and I was trying to reproduce my workflow I had
> with FS5.3.
>
> To visualize statistical maps, I had always used
This was fixed in 7.11. You can use that version or copy the attached
file to this location
$FREESURFER_HOME/matlab/freesurfer_read_surf.m
On 5/11/2021 2:28 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
Hi,
I am using Matlab R2014a, and FS7.1.0
and receiving this error when I
This is because it takes two passes through the transform. One takes
each target vertex and finds the closest source vertex. The other takes
each source vertex not already sampled and finds the closest target
vertex to make sure that every source is represented. With the 2nd step,
there may be
Can you run
mri_info /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz
On 5/10/2021 1:00 PM, Lara Foland-Ross wrote:
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Hello,
I'm trying to run Freesurfer7.1 on docker. I have a macbook air with an apple
chip with BigSur as the OSX.
To test out the
Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>> wrote:
Try
cd yoursubjectname/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3
--label_right_white 41 --label_right_ribbon 42 --save_ribbon
yoursubjectname
On 5/3/2021 4:31 PM, Caspar M. Schwiedr
refers to- for
future reference? When is it best to go through fsaverage?
Thank you for the information
BW,
Marianna
*Από:* freesurfer-boun...@nmr.mgh.harvard.edu
εκ μέρους του Douglas N.
Greve
*Στάλθηκε:* Δευτέρα, 10
did you draw the labels on each subject separately? In that case there
is no need to go through fsaverage.
Projfrac is the fractional distance between the white and pial surfaces
(0.5 is half way)
projdist is the absolute distance (eg, 1.5 is 1.5mm)
Generally projfrac is preferred as it adapts
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