> Dear Freesurfer developers,
>
> I encountered a problem when I tried to open the sample-001. with information
> as follow:
>
> ERROR: Invalid FreeSurfer license key found in license file
> /Applications/freesurfer/license.txt
> If you are outside the NMR-Martinos Center,
> go to http://su
Dear Freesurfer developers,
when I tried to perform example 3: perform a full recon-all on a preexisting
subject folder
The error occurs as follow:
syntax error near unexpected token `newline’
I don’t know how to proceed further.
please help.
Thanks.
Best Regards,
Danny Deng
> Begin forwar
Do you just want to do an ROI analysis? Or do you want to do a
voxel-based analysis? If ROI-based, then follow the steps on the ROI
tutorial (ie, aparcstats2table and mri_glmfit with --table input).
On 11/3/17 4:08 PM, Bruce Fischl wrote:
Hi Mohamed
Doug is away this week and can give you a
Do you have read permission to that file?
On 11/5/17 8:08 AM, Danny Deng wrote:
Dear Freesurfer developers,
I encountered a problem when I tried to open the sample-001. with
information as follow:
ERROR: Invalid FreeSurfer license key found in license file
/Applications/freesurfer/license.
Hello,
I am attempting to extract lGI values (i.e., similarly to *.stats in
#SUBJ/stats) with the following (generic) command:
$mris_anatomical_stats –a aparc.annot –t pial_lgi –f
#SUBJ/stats/lh.aparc_lgi.stats #SUBJ lh
However, this newly generated lh.aparc_lgi.stats is the exact same as the
Dear Freesurfer developers,
I would like to run Local Gyrification Index analysis for a group of
healthy controls and a single patient. After running recon-all -s
-localGI command, we get lh.pial_lgi and rh.pial_lgi surf files. In the
last stage of this analysis, local gyrification index values
try looking here to submit a bug report with information that we can use
to help you
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On 11/5/17 8:17 AM, Danny Deng wrote:
Dear Freesurfer developers,
when I tried to perform example 3: perform a full recon-all on a
preexisting subject
Can you send the command line you are using and the full terminal output?
On 11/2/17 3:09 PM, lanbo Wang wrote:
Dear Freesurfer experts,
When I try run mris_apply_reg according to Xhemi:
"the error is lh.map.mgh does not exist or is not readable by you"
lh.map.mgh is made by which step?
Thank
Look in the recon-all.log file for the command that generates the
aseg.stats file. Use that command but change aseg.mgz to whatever your
mask is (and change the output). Don't include the LUT on the command line.
On 11/1/17 10:24 PM, Ehsan Tadayon wrote:
Hello FS experts,
I'm trying to get t
Dear FreeSurfer list,
My name is Rosalia and this is the first time I post an email on your list.
I have never run FreeSurfer before and I have a doubt regarding the
converting process.
For every T1 folder, I have 192.ima files. I do not know how to pass from
this point to .mgz. It seems that in
Dear Mohamad,
You're right, after I use version 6.0, it works. Thanks for your help.
best,
Lanbo
On Fri, Nov 3, 2017 at 3:12 PM, Alshikho, Mohamad J. <
malshi...@mgh.harvard.edu> wrote:
> Hi Lanbo,
>
> You need Freesurfer 6 to run this command. The flag --src-label is not
> part of FS5.3
>
>
>
Dear Douglas,
The comman line and terminal output show is this:
[mtobia@localhost subjects_results_symptom]$ mris_apply_reg --src
lh.map.mgh --trg lh.map.lh.fsaverage_sym.mgh \
> --streg $SUBJECTS_DIR/s02_base/surf/lh.fsaverage_sym.sphere.reg
$FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.
Hi Rosalia
you give a *single* one of your 192 .ima files to recon-all with the -i
switch. It will figure out all the other files in your volume and process
them. You could also give it a .nii.gz file as well, but in general we
like to start with the dicoms if possible
cheers
Bruce
On Sun, 5
Dear FDs,
According to the instructions, I have cut the 4 lines between the “CUT HERE”,
copy and past the 4 lines into my license.txt file in the home directory to
freesurfer folder as follow:
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