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Bruce,
this is the output:
mri_info wm.mgz
Volume information for wm.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.00, 1.00, 1.00
type: UCHAR (0)
fov: 256.000
dof: 0
can you run mri_info on it? And please include the full screen output
including the command line that you run as well as what it produces.
thanks
Bruce
On Fri,
24 Aug 2018, Davide Momi wrote:
External Email - Use Caution
Yes, I meant the second one and rh.aparc.annot (not l
External Email - Use Caution
Yes, I meant the second one and rh.aparc.annot (not lh) given that as you
said I specified rh.
As for the ls -l on wm.mgz this is the output:
-rw---@ 1 davidemomi staff 432151 Jun 13 2017 wm.mgz
Thanks
Il giorno ven 24 ago 2018 alle ore 17:
Hi Davide
do you mean $SUBJECTS_DIR/mri or $SUBJECTS_DIR/60_AV/mri? It should be the
latter, not the former. Also, can you send us the output of ls -l on the
wm.mgz? And finally, you probably want to use rh.aparc.annot not
lh.aparc.annot since you specified rh on the command line
cheers
Bruc
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Dear Bruce,
thanks for your response.
my SUBJECTS_DIR is set to: /Users/davidemomi/Downloads/Broad_60_AV, which
is actually where the output of recon-all is located.
the file wm.mgz exists and is in the $SUBJECTS_DIR/mri directory
Thanks again
Hi Davide
does that file exist? What is your SUBJECTS_DIR set to?
cheers
Bruce
On Fri, 24 Aug 2018,
Davide Momi wrote:
External Email - Use Caution
Dear FreeSurfer,
I have a problem when I use mris_anatomical_stats. It gives me an error saying
that it couldn't read
the i
External Email - Use Caution
Dear FreeSurfer,
I have a problem when I use mris_anatomical_stats. It gives me an
error saying that it couldn't read the input volume which is the
wm.mgz file.
would you please help me how I should fix this problem?
this is the command which I used:
Thanks Bruce, this did it.
-jared
> On May 4, 2017, at 12:33 PM, Bruce Fischl wrote:
>
> I see. This is the problem - mris_sample_parc is one of the binaries that
> requires all options come before the mandatory arguments. Move the -ct
> part to the beginning and it should work
>
> cheers
I see. This is the problem - mris_sample_parc is one of the binaries that
requires all options come before the mandatory arguments. Move the -ct
part to the beginning and it should work
cheers
Bruce
On Thu, 4 May 2017, Jared P
Zimmerman wrote:
mris_sample_parc ${sub} \
lh ${targ}.n
mris_sample_parc ${sub} \
lh ${targ}.nii.gz \
${targ}_fs6_annot.annot \
-ct ${SUBJECTS_DIR}/${sub}/bla_test_table.txt
This is the call from my script, which didn’t get written to stdout. The
bla_test_table.txt exists, and is just a space delimited file with “index name
sorry, I don't see the mris_sample_parc command line. Can you just send
it and the entire screen output?
On Thu, 4 May 2017, Jared P Zimmerman
wrote:
That’s what I did below, see the script and log.txt attached to a previous
email. This is the output from the mris_sample_parc step
reading
fwiw, this problem persists in FS6.0
-jared
> On May 4, 2017, at 12:11 PM, Jared P Zimmerman
> wrote:
>
> That’s what I did below, see the script and log.txt attached to a previous
> email. This is the output from the mris_sample_parc step
>
>> reading parcellation volume from
>>
That’s what I did below, see the script and log.txt attached to a previous
email. This is the output from the mris_sample_parc step
> reading parcellation volume from
> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz...
> reading input surface
>
can you try it with -ct
and send us the output if that doesn't work? That's what we use
internally
cheers
Bruce
On Thu, 4 May 2017, Jared P
Zimmerman wrote:
Yeah I see that, but the cma_parcellation_colors.txt isn’t distributed with FS
5.3, yet it is the default LUT called by mris_sample_
Hi Jared
it looks like it couldn't find the lookup tbale:
reading input surface
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white...
could not open translation file
/share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt
cheers
Bruce
On Thu,
4 May 2017, Jared P
Zimmerman
Hey Bruce et al, any update on this?
Thanks,
Jared
> On Apr 28, 2017, at 2:48 PM, Jared P Zimmerman
> wrote:
>
> Here’s the script that I’m running and the merged stderr stdout. I’ve also
> tried various permutations of mris_sample_parc using the -t flag and using
> different LUTs than the
Here’s the script that I’m running and the merged stderr stdout. I’ve also
tried various permutations of mris_sample_parc using the -t flag and using
different LUTs than the one I made. Also copying the log here incase the text
files get removed.
Thanks,
jared
./targetAnnotStats.sh: line 21
Hi Jared
can you send us the full command line and screen output?
cheers
Bruce
On Wed, 26 Apr
2017, Jared P Zimmerman wrote:
Any chance I could get some help on this? still having this problem
On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman
wrote:
Hi FS Experts,
I’m having tro
Any chance I could get some help on this? still having this problem
> On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman
> wrote:
>
> Hi FS Experts,
>
> I’m having trouble getting anatomical stats from a parcellation I made out of
> scanner-space volume ROIs. I have taken the following steps to
Hi FS Experts,
I’m having trouble getting anatomical stats from a parcellation I made out of
scanner-space volume ROIs. I have taken the following steps to do this.
mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o
myROI_orig.nii.gz --interp nearest
mris_sample_parc Subj111 lh myR
Hi Ed
was there any error message or anything? It just seems to end normally
but then gives a nonzero exit code causing recon-all to stop?
cheers
Bruce
On Mon, 13 Feb
2017, Gronenschild Ed (NP) wrote:
> Hi,
>
> All datasets that I've processed sofar with v6 resulted in exactly the same
> erro
Hi Mahtab
the mris_anatomical_stats help says:
mris_anatomical_stats [options] []
.
.
.
-f
table output to tablefile (different format than -b).
Must use-a or -l options to spec input.
.
.
.
so you are specifycing the name of the table as "anon", the n
Dear Douglas,
The wm.mgz is in the mri folder so it's in:
Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz.
Best Regards,
Mahtab.
Sent from myMail for iOS
Thursday, May 19, 2016, 16:19 +0100 from gr...@nmr.mgh.harvard.edu
:
>The second one is a valid command (1st is not). Wh
The second one is a valid command (1st is not). What is the full path to
the wm.mgz file that is in your anlayzed data?
On 05/19/2016 10:33 AM, Mahtab Farahbakhsh wrote:
> Dear Bruce,
>
> This is the input command and the output that I get:
>
> bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA4
please send the command line and all terminal output
On 05/19/2016 05:50 AM, Mahtab Farahbakhsh wrote:
> Dear FreeSurfer,
>
> I have a problem when I use mris_anatomical_stats. It gives me an
> error saying that it couldn't read the input volume which is the
> wm.mgz file. would you please help
Dear Bruce,
This is the input command and the output that I get:
bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA45.label -f anon lh anon
lh
limiting computations to label anon/label/lh.BA45.label.
reading volume
/Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz...
mghRead(/Appl
Hi Mahtab
can you please send the screen output of the command you ran and what it
printed, and also what the environment variable SUBJECTS_DIR is?
cheers
Bruce
On Thu, 19 May 2016, Mahtab Farahbakhsh wrote:
Dear FreeSurfer,
I have a problem when I use mris_anatomical_stats. It gives me an e
Dear FreeSurfer,
I have a problem when I use mris_anatomical_stats. It gives me an error
saying that it couldn't read the input volume which is the wm.mgz file.
would you please help me how I should fix this problem?
Best Regards,
Mahtab.
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