I still receive the same error message (1mm is now 2mm in the message).
outanadir =
/autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask2
Error using MRIread (line 76)
ERROR: cannot determine format of
/autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53
?
On 10/03/2013 10:29 AM, SHAHIN NASR wrote:
Hi Doug,
Did you have a chance to find the reason for this problem?
On Wed, Oct 2, 2013 at 3:20 PM, sha...@nmr.mgh.harvard.edu
mailto:sha...@nmr.mgh.harvard.edu wrote:
I still receive the same error message (1mm is now 2mm in the
message
02:34 PM, SHAHIN NASR wrote:
Hi,
When I run selxavg3-sess, I face this error:
ERROR: cannot find volume matching
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg
ERROR: loading nonpar reg
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2
-refeventdur 14 -force -fsd bold_Color
-per-run
But using -mcprextreg flag generates an error. Is it a bug?
There is not an mcextreg file there. There is mcprextreg file. I think
you need to run preproc with -per-session to get the mcextreg file
doug
On 03/18/2014 02:34 PM, SHAHIN NASR wrote:
Hi
-nconditions 8 -refeventdur 14 -force -fsd
bold_Color
-per-run
But using -mcprextreg flag generates an error. Is it a bug?
There is not an mcextreg file there. There is mcprextreg file. I
think
you need to run preproc with -per-session to get the mcextreg file
doug
On 03/18/2014 02:34 PM, SHAHIN
?
There is not an mcextreg file there. There is mcprextreg file. I
think
you need to run preproc with -per-session to get the mcextreg file
doug
On 03/18/2014 02:34 PM, SHAHIN NASR wrote:
Hi,
When I run selxavg3-sess, I face this error:
ERROR: cannot find volume matching
/autofs/cluster/tootell
Hi,
I have two questions about mri_segstats. I want to measure the surface
area of a functionally-defined ROI. I used the mri_segstats as below
and I want to be sure that it is correct. Please note that ROIs were
defined in the native space.
mri_segstats --i $SUBJECTS_DIR/SBJ1/surf/rh.area
wanted to collect that.
doug
On 02/25/2013 02:39 PM, SHAHIN NASR wrote:
Hi,
We are planning to collect high resolution _functional_ MRI for a
group of subjects with voxel size smaller than 1 mm. For these
subjects, we already have reconstructed _anatomical _scans with 1 mm
voxel size
I want to compare 2 different experimental conditions that were
scanned within different runs. For example assume that, in ten runs I have had
conditions 1 and 2 and in another ten runs I have had condition 3 and 4. Now I
want to compare condition 1 and 3. Is it possible?
Regards Shahin
Hi everyone
For my old subjects I already have aparc.2005 atlas file in the label
directory but not the 2009a version. I want to know how can I make 2009 version
for these subjects without doing the recon-all for them.
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center
Hi Doug and freesurfers,
My subjects have participated in two independent experiments within two
different sessions (e.g. experiment 1 in day 1 and experiment 2 in day 2).
Now I
want to see if the contrast between conditions of experiment 1 and 2 is
significant or not. For instance I
Hi,
Would you tell me how can I see time-course of activities within one ROI
(averaged over voxels) for each experiment condition? Should I use matlab
commands?
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
or surface and how
significant the difference is?
Regards Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Hi Freesurfers,
Anybody knows how can I make lh and rh.annotation.aparc files for a monkey?
I
need them initiate an brain averaging process.
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
Thanks Bruce,
To avoid this problem, is there anyway to run make_average_subject without
having lh and rh.aparc.annot files?
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
From: Bruce Fischl fis
saying
that I don't have a lh and rh.aparc.annot files.
Apparently very old versions of freesurfer (version 3) didnt need these
files. Am I right? Do you suggest to use old versions?
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
Ok now I faced another problem saying that I dont have talairach.xfm for
monkeys. Would you tell me how can I generate it for monkeys?
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
From: Douglas N Greve gr
.predict.label
Would you tell me what is the possible error/problem?
P.S.: I used both ver 4.5 and 5.0 and the result was the same.
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Hi Surfers
We are wondering if we can use freesurfer to analyze ECG-gated fmri. As
far as I see, mkanalysis-sess expects a fix TR. Since we are in the
design stage, any hint or suggestion to facilitate future data analysis
will be highly appreciated.
Regards
Hi Adil,
My understanding is that, you can always change the location of
SUBJECTS_DIR. Just use this command:
setenv SUBJECTS_DIR
You do not need to mention this new address in your recon-all command.
Good luck
> HI,1-I'm working with FreeSurfer that is on a server. I don't have
>
Hi Bruce,
Would you be more specific. The command that you suggested generates
?h.white.K and ?h.white.H. I am trying to generate ?h.curv.
> try running
>
> mris_curvature -w ...
> On Wed, 30 Aug 2017,
> sha...@nmr.mgh.harvard.edu wrote:
>
>> Dear Freesurfers,
>>I want to project a map
Dear Freesurfers,
I want to project a map on up-sampled inflated brain. Up-sampled
inflated brain has been generated using mris_mesh_subdivide command
(without any problem). But when I apply the same command to ?h.cuv I
get an error message that:
ERROR: MRISread: file 'surf/rh.curv' has
Dear Experts,
We are looking for a way to measure the amount of overlap between each
'aparc 2009 segment' vs. 'Yeo 7 networks segments'. Currently I can do
that by converting segments to labels and and then measuring the number
of common vertices between them. But I was wondering if there is a
d lta files. If no, would
>> you tell me how to extract regmat from this lta file.
>>
>> regards
>> _
>>
>> Shahin Nasr
>>
>> Assistant Prof. in Radiolo
if there is
an updated version of fmri_readreg.m to read lta files. If no, would
you tell me how to extract regmat from this lta file.
regards
_
Shahin Nasr
Assistant Prof. in Radiology
Harvard Medical School
Martinos Imaging Center, MGH
Bldg 149, 13th street,
Charlestown
it is not the same as cnr.nii
generated by selxavg3-sess for the same subject.
Regards
_
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
Bldg 149, 13th street,
Charlestown, MA 02129
Your problem solved?
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addressed. If you believe this
Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
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=1, then i see the
difference and niters=1.
My question is, why is fwhm = 0.66 not acceptable? How can i solve this
issue.
Regards
_
Shahin Nasr
Assistant Prof. in Radiology
Harvard Medical School
Martinos Imaging Center, MGH
Bldg 149, 13th street
; (niters=0). When I use the same command with fwhm =1, then i see the
>> difference and niters=1.
>>
>> My question is, why is fwhm = 0.66 not acceptable? How can i solve this
>> issue.
>>
>> Regards
>>
>> _
>>
Hi Surfers,
I am trying to use freeview to present retinotopy mapping in
subcortical regions. I need to show complex (real and imag) values
generated by a retinotopy analysis in a 'color wheel' format (similar
to what tksurfer does).
Any hint?
_
Shahin
Hi,
I want to generate a map to show the significant difference between
HRF undershoot (negative peak of activity) between two conditions
independent from the positive peak. Is there anyway, to generate this map?
P.S.: Please note that I need a map and not a time course graph.
--
Shahin
That's the problem Doug. I have already generated the FIR model but how can
I show the sig MAP for one particulat time point. What are the other
ways?
On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Hi Shahin, there are several ways that you could do
already generated the FIR model but how
can
I show the sig MAP for one particulat time point. What are the other
ways?
On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu**wrote:
Hi Shahin, there are several ways that you could do it. The one that
immediately comes
the problem Doug. I have already generated the FIR model but how
can
I show the sig MAP for one particulat time point. What are the other
ways?
On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu**wrote:
Hi Shahin, there are several ways that you could do
Hi,
Would you tell me where I can find cvs_avg35 brain template.
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PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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1.25 -mcextreg -TR 2.000
-nconditions 3 -refeventdur 14 -force -runlistfile RunList -per-run -fsd
bold -no-mask
I get this error:
outanadir =
/autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask
Error using MRIread (line 76)
ERROR: cannot determine format
-a RetinaPrj_New
I am also attaching the analysis.info
If you want to test the files, you can see the subject files in:
/autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir
Note: I did all of these tests from scratch after deleting files from the
previous tests. So it can't be due to a remaining
to manually
average the .dat files? Should we consider anything in this averaging?
Thanks
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PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Hi Surfers
I have done a surface-based group-averaged mapping and now I need to
save the results of the mri_glmfit (sig.nii) command in GIFTI .func.gii
format. Does mri_glmfit support this output format?
Regards
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
, then:
1) Can I apply the same command to ces.nii file to have the absolute value
of the effect size (i.e. abs(C1-C2 effect size)) or should I consider other
factors?
2) Do I need to apply the same routine to cesvar?
Thanks
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
run selxavg3-sess, it returns an error that
cannot determine format of
test/bold/013/fmcpr.sm1.5
and exits. Would you tell me why those files are not generated?
Regards
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
Hi,
When I run selxavg3-sess, I face this error:
ERROR: cannot find volume matching
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg
ERROR: loading nonpar reg
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg
Hopefully this is the last problem with per-run analysis (in native space)
but as far as I see, preproc-sess and selxavg3-sess do not generate
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/register.dof6.dat
Because of that, when I use tksurfer-sess it faces an error
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PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Hi,
I was wondering if I can average two scan sessions with different TRs
or not. Number of conditions and all other factors are exactly the same
between the two sessions.
regards
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--
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PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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this possibility or not.
If yes, then I appreciate if you can introduce me a reference (published
article) to support our answer.
Regards
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PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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previous but nobody answered (see the link
below)
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024394.html
Regards
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Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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.
On Wed, Oct 24, 2012 at 1:00 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Hi Shahin, you can do seed-based analysis. In principle you can do this
with task data, you just need to adjust your conclusions accordingly. There
is no easy to way to only do the analysis on the resting epochs
1.25 -mcextreg
-TR 2.000 -nconditions 7 -refeventdur .10 -fsd bold -per-run -force
This time when I ran selxavg3-sess command I faced this error:
ERROR: cannot determine format of
/autofs/cluster/tootell/pitcairn/1/shahin/Reward/Subjects/limi1/bold/004/fmcpr.sm5
(MRIread)
Error
Hi,
I have faced a problem using ROI-based, fcseed-config and fcseed-sess
I used either:
fcseed-config -roi
/cluster/tootell/pitcairn/1/shahin/good_subjects_anat/atou_anat/label/rh.V1.label
-fcname mean.R_V1.dat -fsd bold -mean -cfg mean.R_V1.config
OR:
fcseed-config -roi
/cluster/tootell
Hi
I want to know if there is any limit for the automatic registration of
functional scans on structural ones when we are scanning activity just in
a specific part of the brain (e.g. occipital cortex).
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Hi,
Would you tell me how can I use isxconcat-sess to calculate group
averaged partial correlation coefficient map? I have already generated
pcc.nii files for each individual subject.
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
Hi,
Is there anyway to print multiple contrasts in one output file using
funcroi-table-sess command?
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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(am I
right?). Would you tell me how can I fix this problem?
P.S.: please note that sequence of subjects and all MRI parameters are
exactly the same between the two maps.
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
-sess for either map1 or map2. Right?
On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Hi Shahin, it is not as simple as doing a subtraction of the cesvar files.
What you are trying to get is the expected variance of your difference
between the ces files
be roughly the sum of the dofs of the individual subjects. Why
are you using a fixed-effects model?
doug
SHAHIN NASR wrote:
Thanks Doug. Just one related question. Should I also generate a new
ffxdof.dat file for this map? I assumed that ffxdof depends on the number of
subjects (session
Hi Surfers,
It is my first experience with Event-related paradigms. In my
experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum
variable delay between trials to be able to analyze data without any
confound.
Regards
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos
...@nmr.mgh.harvard.eduwrote:
Hi Shahin, there are several ways to answer this question. If you are
going to analyze assuming a shape to the HRF, then the actual delay between
stimuli is technically not important (though 4s will be good to avoid
attenuation in the following stimulus). If you're using an FIR model
.
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Hi
In monkey fmri, we usually have to do the functional-anatomical
registration manually since bbregister doesn't work very well.
It was easy in version 4.5 since we usually used just one run for
registration. In version 5.1 we can use per-run option to improve
registration but I am
if it increases the registration time.
Regards
P.S.: using --t2 in bbregister (instead of --bold) generated the same
outcome but --t1 was completely off.
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
0.1572 0.2675
1.4203 1.1527
How can mean=941.0988 when the max=1.4203 ???
Regards
--
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PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Martinos Imaging Center, MGH
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version of our MRA and how good
it was when we used T1+pial registeration:
tkregister2 --mov
/cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_500_pre_contrast/010/001_nu.nii
--reg
/cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_500_pre_contrast/010
that
registration to the partial FoV assuming that the whole and partial share a
scanner space (which they will if acquired at the same time). The
intermediate can be anything, eg, fMRI, anatomical, B0 map, low-b DTI
volume.
doug
On 09/30/2014 12:41 PM, SHAHIN NASR wrote:
Hi Doug,
Sorry
://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Hi,
For one of my subjects, I have noticed a misalignment between sig.nii
and orig.mgz when I try to show the sig map using either tkmedit (as below):
cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Analysis
tkmedit-sess -s ../Subjects/auil2 -a OriExp_TR3_1p5mm_PR -c ANG_90_45
/mri_fwhm --mask
/autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz
--i
/autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz
--o
/autofs/cluster/tootell/pitcairn/1/shahin
Hi Surfers,
I need to measure the ''minimum' distance between a cortical vertex and
a manually defined path (e.g. V2-V3 border). Is there any command or
straightforward way to do that?
Thanks
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
I need
to do for the regressor!
A sample regressor file is attached. It has 98 rows corresponding to 98
TRs that we have in the experiment!
Regards
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PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
ShockNUI_Fin
Description: Binary data
in seconds of the time points you want to
exclude.
doug
On 5/1/15 11:45 AM, SHAHIN NASR wrote:
Hi Surfers
I want to remove the possible effects of a binary noise (electric
shock) from the evoked fMRI. To do so, I have generated a regressor
file in which all TRs in which electric shock has been
/cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz
Regards
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PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Hi Doug,
It works without any error.
Thanks a lot
On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
I just made a fix. Can you try it out and let me know if it works?
On 05/14/2015 11:38 AM, SHAHIN NASR wrote:
Hi,
Does anyone know what has changed
.: The command that I use it like this:
mris_pmake --subject Sbj --hemi lh --surface smoothwm --mpmProg pathFind
--mpmArgs vertexStart:Vert1,vertexEnd:Vert2 --mpmOverlay euclidean
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
Hi Freesurfer developers,
As far as I see, pRF (population receptive field) mapping is not a part
of current freesurfer (please correct me if I am wrong). I was wondering
if you have any plan to add it to the next/upcoming freesurfer version?
Regards
--
Shahin Nasr
PhD in Cognitive
Hi Surfers and Doug,
I was trying to average two scan sessions of the same subject and
isxconcat-sess under dev-env failed again. This time I get this message:
ERROR: cannot find
/autofs/cluster/tootell/pitcairn/1/shahin/FeatureAttention_Color/Subjects2/hron1/bold/Attention_TR3_FHWM0_PR_Ver2
Dear Surfer,
I want to cite the methods used in mris_pmake command but I can't find
it in wikisurfer or the help of this command. Is the method used in this
command described in a published paper?
Regards
--
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard
Hi Surfers,
I have faced an issue with preproc-sess and I appreciate your help. I
have a single slice EPI scan (number of TRs > 500; TR=0.2). When I tried to do
preproc-sess, mc-afni2 is called and it crashed. When I checked the log, I
noticed this:
3dvolreg.afni -verbose -dfile
Hi Surfers,
Is there anyway to pass the full address of a surface to mri_vol2surf? To
clarify, we are using surfaces that are saved outside /surf/ and we prefer
not to relocate them every time that we want to use mri_vol2surf.
Thanks
___
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Friday, July 17, 2020 1:04 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] rtview - loading a tcl file
ok, try now
On 7/17/2020 12:49 PM, Nasr, Shahin,Ph.D. wrote:
Thanks. But as far as I
Hi Surfers,
I was wondering if there is a way to load a tcl file with rtview command.
Specifically, I need to change the color table to RYGB, remove the aparc, ... .
Thanks
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s N. Greve
Sent: Friday, July 17, 2020 12:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] rtview - loading a tcl file
I just added --tcl to rtview. The new version is in dev
On 7/17/2020 12:23 PM, Nasr, Shahin,Ph.D. wrote:
Hi Surfers,
I was wondering if there is a way to load
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] rtview - loading a tcl file
What is the tksurfer command that is output?
On 7/17/2020 1:13 PM, Nasr, Shahin,Ph.D. wrote:
Unfortunately it is not working. My command is like this:
rtview --s SUBJ --real real.nii --imag imag.nii --eccen --hemi lh --fsig
: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Friday, July 17, 2020 1:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] rtview - loading a tcl file
sorry, they again
On 7/17/2020 1:27 PM, Nasr, Shahin,Ph.D. wrote:
tksurfer SUBJ lh inflated -aparc -tcl
: Friday, July 17, 2020 1:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] rtview - loading a tcl file
OK, try again:)
On 7/17/2020 1:42 PM, Nasr, Shahin,Ph.D. wrote:
the tksurfer look correct as below
tksurfer SUBJ lh inflated -aparc -tcl
/usr/local/freesurfer/dev/lib/tcl
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Nasr, Shahin,Ph.D.
Sent: Wednesday, July 22, 2020 12:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] tksurfer - failed to calloc
Hi Surfers,
I get the following error when I use tksurfer for one of our subjects
Hi Surfers,
I get the following error when I use tksurfer for one of our subjects:
znzTAGskip: tag=1830834290, failed to calloc 1834378240 bytes!
To clarify, this error is only limited to freesurfer version 6.0 and 7. But
version 5.3 works fine with the same subject.
Regards
irrespective of the Start/End vertex, as far as I see. I
guess this error is because a file in the subject's brain recon is corrupted.
But unfortunately, the error message is not helpful. I even tried to open the
error.log. But I do not see any further info there.
Any suggestions?
Shahin
or freeview -f
On 11/12/2020 9:52 AM, Nasr, Shahin,Ph.D. wrote:
Hi Surfers,
For one subject, when I run mris_pmake as below:
mris_pmake --subject --hemi lh --surface smoothwm --mpmProg
pathFind --mpmArgs vertexStart:,vertexEnd:
--mpmOverlay euclidean
I get the following error:
mris_pmake
: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce R.,PHD
Sent: Friday, April 7, 2023 5:11:49 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
External Email - Use Caution
Hi Shahin
What is your command line? mris_flatten does some
External Email - Use Caution
Correct Luis. But I am not sure why did verion 7 act like this.
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
https://secure-web.cisco.com/1dieRkuIGIwcoRKWXF1_E_U5H9RTe
=1:overlay=/sig.nii.gz:overlay_threshold=2,4 -viewport 3d -zoom 1.2 -cam Elevation 90
Regards,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
https://mesovision.martinos.org/
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