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Hi experts,
I want to do some research on the cortical thickness of visual cortex using FS
6.0. Is there specified or associated cortex model for the segmentation of
visual cortex?
Thanks for your reply in advance. I need your help.
Sincerely,
Zheng
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Hi FS experts,
I'm running a longitudinal process with three time points per subject and was
wondering if you can advise on the typical time to process? Can the -parallel
flag be added to the base and long steps? I'm running this on a cluster that
Hi Zheng
if you mean primary visual cortex, then you can use our estimate of BA17
which is stored in the subject's label subdirectory (as are BA18 and MT).
If you mean all of visually-responsive cortex I don't think we have
anything (nor is that a terribly well-defined concept, since some of i
On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
>
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> Hi Douglas,
>
> Thank you for answering. Please find below new questions.
> Bien cordialement,
>
>
> Le ven. 30 nov. 2018 à 00:00, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> a écrit :
>
For it to show up in the output file, the cluster-wise pvalue must be <
.05 (CWT). To see all the clusters regardless of significance, run it
with a CWT of 1. If you want to run with a more liberal cluster forming
threshold (CFT), you can try using permutation. See
http://freesurfer.net/fswiki/
If you just want to look at the difference maps, you can load the
mris_preproc output stack as an overlay, then scroll through each one of
them. You're still looking at each one of them, but you don't have to
open them up one-by-one.
On 12/05/2018 02:21 PM, Sims, Sara A wrote:
>
> Exter
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Dear FreeSurfer experts,
I am encountering a problem when trying to downsample to fsaverage6 with FreeSurfer v.6.(see below):
mri_surf2surf --srcsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s --srchemi lh --srcsurfreg fsaverage6.sphere.reg --tr
You can tell from the sign of the "VtxMax" column that indicates the
maximum in the cluster. If you used a signed test (pos or neg), then
they will all have the given sign. If you used an unsigned test (abs),
then they may have different signs.
On 12/04/2018 11:54 AM, Backhausen, Lea wrote:
>
You can use
mri_binarize --i aparc+aseg.mgz --match 1028 --o
ctx-lh-superiorfrontal.nii.gz
See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
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>
> Hello,
>
> Is there a command to extract R
On 12/04/2018 02:17 PM, T and LS wrote:
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>
>
> Dear Help Desk - I have a few basic questions about freesurfer. I am
> retired military bomb technician working on a blast TBI initiative and
> not a research so please bear with me. We are looking at a lo
Is this a volume label that is supposed to be on the cortical ribbon? An
you wan to do a surface-based dilation? Or do you just want to dilate it
in 3D?
On 12/04/2018 08:28 PM, Mareike Grotheer wrote:
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> Hello FreeSurfer Developers,
>
> I am trying to
Can you send the full terminal output?
On 12/05/2018 01:25 AM, Sara Jafakesh wrote:
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>
>
>
>
>
>
> Dear freesurfer experts,
> I want to calculate corrolation between two seeds with
> freesurfer-linux-centos6_x86_64_stable_pub-v6 .aft
Can you be more specific about which files you want to map into your DWI
space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You
will need a registration file which you can obtain with bbregister
On 12/05/2018 02:34 AM, Maedeh Khalilian wrote:
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It is possible to use octave instead with
export FS_USE_OCTAVE=1
You must have octave installed of course
On 12/05/2018 02:38 AM, Maedeh Khalilian wrote:
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>
> Dear experts,
> Is it necessary to install Matlab to use FsFast for functional
> connectivity?
> T
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Hi Greve,
It is a volume label that is supposed to be on the cortical ribbon. I want
to perform surface-based dilation.
Thank you,
Mareike
On Thu, Dec 6, 2018 at 9:11 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
>
> Is this a volume l
sorry, we don't have a hippo cortex analysis method
On 12/05/2018 10:26 AM, Yixin Ma wrote:
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> Hi Freesurfer experts,
>
> After running the segmentation of hippocampus subfields, I'm wondering
> if I can get the surface of the gray matter and white matter
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Hi Dr Greve,
> I tried to follow this web page
> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> This tutorial seems to be for cortical thickness data. After sampling each
> individual's surface onto the average surface, how can I modify t
Try using mris_apply_reg. The command line is simpler (but otherwise
gives the same result).
On 12/06/2018 11:44 AM, Sanfelici, Rachele wrote:
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> Dear FreeSurfer experts,
>
>
> I am encountering a problem when trying to downsample to fsaverage6
> with F
If you have not sampled the PET data onto the surface, you will need to
run mri_coreg to create a registration to the anatomical. Then use can
use mris_preproc with the --iv option (listing each subject with a
different --iv). Run mris_preproc with --help to get examples
On 12/06/2018 12:31 PM,
On 12/03/2018 03:14 PM, Zhi Li wrote:
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>
> Hello FreeSurfer Experts,
>
> Now I have a custom annotation file (only the cortical surface). May I
> ask how could I use it to extract the mean time series from the
> fsfast-preprocessed fMRI data? I have tried
Use mri_segstats. Run with --help to get more info
On 12/03/2018 06:12 AM, Anik Dar wrote:
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> Dear All,
>
> I have segmented the midbrain of each subjects into different
> subregions (peduncle, substantia nigra, red nucleus etc) using an
> atlas. I am tr
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Hi Dr Greve, yes exactly this is what I did. i user mri_corg and I got the
reg.lta file. Then I used mris_preproc with the flag --iv but this output an
error message that the flags --fsgd, paired-diff and --iv doesn't work
together. This is the reaso
Does the orig.mgz file look ok?
On 11/30/2018 01:14 PM, Figueiro Longo, Maria Gabriela wrote:
>
>
> Hello FreeSurfer Developers,
>
> I'm attempting to run the longitudinal stream, but in the [LONG] step
> of one time-point of on of my subjects, I have the following error:
>
> MRInormInit():
> INF
what is your $MATLAB variable set to? It should be set to the matlab
executable
On 11/30/2018 01:30 PM, Emily Levin wrote:
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> Hi FreeSurfer experts,
>
> I'm trying to run mkcontrast-sess using the newest development version
> of freesufer from Nov 30th,
If you want to use the --cache-in option, you need to have run recon-all
with the -qcache option. If you take away the -cache-in option, then
mris_preproc should run correctly
On 11/28/2018 12:45 PM, Larissa Bechtle wrote:
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>
> Hi everyone,
> thank you ver
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Hello experts,
I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm 1000 1.3 abs
--cwp 0.05 --2spaces command, but its taking forever even if I reduce # of
permutations from 1000 to 10.
I was just wondering if there’s a version of FreeSurfer f
On 11/27/2018 06:46 AM, C.P.E. Rollins wrote:
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> Hi Douglas,
>
> Thanks a lot for your answers.
>
> 1) For the permutations, would you recommend using this for
> controlling for MC in cortical thickness analyses too?
Yes
> Why is it recommended to use permutation
The 2nd row. The value you want is 3.3455
On 11/27/2018 08:19 AM, C.P.E. Rollins wrote:
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>
> Dear Freesurfer developers,
> I have a quick question regarding calculating mean LGI (Marie Schaer's
> measure) per hemisphere.
> I believe that I can get the mean
On 11/27/2018 02:16 PM, Song, Da-Yea wrote:
>
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>
> Hello,
>
> I had a follow up question regarding the CerebralWhiteMatter variable
> from aseg.stats.
>
> 1.Does this include the white matter underlying the cortex?
>
It includes the all the WM in each hemis
Your command looks right. Sometimes there can be some stretching or
compression of the labels as it is transformed back to an individual,
especially if it is very small. Can you send pics of what you are seeing?
On 11/27/2018 05:19 PM, Wang, Xiaoyu wrote:
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Is that a subcortical GM structure (eg, amygdala)? The path of the
surface in subcort GM structures is unimportant
On 11/29/2018 03:17 AM, Miguel Ángel Rivas Fernández wrote:
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>
> Hi Freesurfer devs,
>
>
> I´m doing a visual quality control of my pial and
Right, you can't use --fsgd. The FSGD file is used to get a list of
subjects, but you have already specified the list with the --iv options.
Does it run properly if you remove --fsgd (but keep --paired-diff)?
On 12/06/2018 12:45 PM, john Anderson wrote:
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yes.
The images have lower SNR but we ran other subjects with similar acquisition
parameters and we didn't have problems.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Thursday, December 6, 2018 3:46:27 PM
To: freesur
I don't know what Slurm is, so I guess the answer is no. If you have
multiple processors on your machine, you can use the --bg option. In
general, I have not seen it take that long to run. How many input
subjects do you have?
On 12/06/2018 12:55 PM, Sahil Bajaj wrote:
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Dear Dr. Greve,
I have 45 subjects as input. SLURM is also a parallel processing pipeline
similar to PBS, Grid Engine, or Condor:
https://en.wikipedia.org/wiki/Slurm_Workload_Manager
I am not sure how can I speed up the mri_glmfit-sim processing.
Than
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Thanks Dough for your suggestions. I tried to use permutation method, but
its giving me following error:
ERROR: design matrix is not orthogonal, cannot be used with permutation.
If this something you really want to do, run with --perm-force
Can you
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Thank you for your kind reply. Sorry for the confusing question. Now I have
an annotation file in fsaverage space. And I want to extracted mean time
series from each roi in this annotation file from preprocessed fMRI data,
e.g. fmc.odd.sm5.fsaverage.lh.
The easiest thing would be to run
mri_segstats --annot subject lh yourannot --excludeid 0 --i
fmc.odd.sm5.fsaverage.lh.nii.gz --avgwf avgwf.dat
avgwf.dat will have a row for each fmri time point and a column for each
parcellation
On 12/06/2018 01:45 PM, Zhi Li wrote:
>
> External Emai
did you do this?
First, install a new version of mri_glmfit-sim from
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/mri_glmfit-sim
(copy it to $FREESURFER_HOME/bin and make it executable with chmod a+rx
mri_glmfit-sim).
On 12/06/2018 01:28 PM, Martin Juneja wrote:
>
>
I think something is wrong if you only have 45 subjects, it should not
take that long. Can you send your mri_glmfit command line and the
terminal output of mri_glmfit-sim?
On 12/06/2018 01:14 PM, Sahil Bajaj wrote:
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>
> Dear Dr. Greve,
>
> I have 45 subjec
On 12/06/2018 02:07 PM, Zhi Li wrote:
>
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>
> Thank you very much, Douglas. It works now. How could I know the ROI
> index of each column in the .dat file?
If you add --sum sum.dat, the sum file will tell you the order
> And if it is available to use pca duri
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Thank you very much, Douglas. It works now. How could I know the ROI index
of each column in the .dat file? And if it is available to use pca during
extracting time series as fcseed-config?
Best,
Zhi
___
Fre
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Thanks Dr. Greve, actually I was using --bg 2 in my command line. Removing
--bg has now speeded up the process.
Thanks again for your help.
Regards,
Sahil
On Thu, Dec 6, 2018 at 12:04 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> I t
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Hi there,
I would like to know if a condition leads to a delayed HRF peaking.
To device an experiment to answer this, I collected finger tapping pilot data
with 80 trials of 3s of tapping, and jittered ITI between 5 to 25 seconds,
TR=1.6.
The tria
Hi Lauri, what is non-ideal about it?
doug
On 12/06/2018 05:30 PM, Lauri Tuominen wrote:
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>
> Hi there,
>
> I would like to know if a condition leads to a delayed HRF peaking.
>
> To device an experiment to answer this, I collected finger tapping pilot data
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Dear FreeSurfer Experts,
I have some baseline and follow-up MRI scans that I would like to process
through the longitudinal stream.
Some of the baseline images were originally in Analyze format (LAS orientation)
and were converted into nifti (keepin
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Hi,
I'm planning a freesurfer analysis of a large MRI dataset, and want to use the
"380 GPU nodes" (and other cores/nodes) on the Palmetto Cluster
(https://www.palmetto.clemson.edu/palmetto/userguide_palmetto_overview.html) to
speed up the process.
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