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
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