See whether this helps. You will have to go in the opposite direction,
but the idea is the same
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 11/12/2018 02:00 PM, Min Zhang wrote:
>
> External Email - Use Caution
>
> Dear Freesufer team:
>
> I have marked bounding box
Can you include the command line and full terminal output? From what you
have below, it says it is only finding one non-null condition, so double
check your par files
On 11/12/2018 04:58 PM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> Thank you!
> I changed the event
I just fixed it
On 11/12/2018 09:35 PM, Bruce Fischl wrote:
> Hi Baxter
>
> we are seeing this locally as well. Probably a bug introduced into
> the last day or two. We will post a fix soon
>
> cheers
> Bruce
>
>
> On Mon, 12 Nov 2018, Baxter P. Rogers wrote:
>
>> External Email - Use Caut
Just run
recon-all -s subject -segstats
and the new ICV should appear in the aseg.stats file
On 11/13/2018 12:08 PM, Gamaliz wrote:
>
> External Email - Use Caution
>
>
> I have a fewT1 scans that have obvious incorrect registration
> to mni_average_305. I opened tkregister2 --s subjid --
e automatically?
>
> On Tue, Nov 13, 2018 at 12:13 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Just run
> recon-all -s subject -segstats
> and the new ICV should appear in the aseg.stats file
>
> On 11/13/2018 12:08 PM,
v.tar.gz
> SHA256 9ea8be61f2f4132770f52459a3e1c746f633727123f9f354953e93466dee165c
> build-stamp.txt freesurfer-linux-centos7_x86_64-dev-20181113-8abd50c
>
> Thanks,
> Baxter
>
>
> Greve, Douglas N.,Ph.D. wrote:
>> I just fixed it
>>
>> On 11/12/2018 09:35 PM, Bruce Fischl wrote:
>>> Hi Baxter
>&g
They are not. You can compute the p-value (10^-abs(sig)), then multiply
it by the number of comparisons
On 11/14/2018 09:18 AM, Ralf Veit wrote:
> External Email - Use Caution
>
> Dear list members,
>
> I run mri_glmfit using the aparc stats tables as input and I got a
> sig.table.dat fi
It looks like you might have a very big defect. Probably there is a bit
of skull or cerebellum still attached. Follow the tutorial for checking
for and fixing defects.
On 11/14/2018 02:59 AM, 1013364183 wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Dear Bruce Fischl
On 11/14/2018 04:00 PM, Yixin Ma wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer experts,
>
> I'm writing to ask about coregistration between a thin oblique coronal
> slab of DTI image ( only 15 slices) and a cubic 1x1x1 voxel size
> anatomical image (volume size is 256x256x25
mri_segstats using your VOI as the arg to --seg. Also include --excludeid 0
On 11/14/2018 06:14 PM, Kim, Jisoo,M.D. wrote:
>
> Hello Freesurfer developers,
>
>
> I am trying to get volume measurements (mm^3) on VOIs (volume of
> interest) that I created on Freeview. All I can do is to export the
Probably it was interrupted and the file as not completely written, or you ran
out of space on the disk. If you start over, does it continue to happen?
On 11/16/18 4:15 PM, Batuhan Erkat wrote:
External Email - Use Caution
Hello,
I am using FreeSurfer solely for reconstruction. I am ha
You can follow the instructions here for the case where you are not using
kinetic modeling. You don't need to do the PVC either
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
This command in particular, you just need to generate the registration and
supply you input as the --mov
mri_vol2vol
High p-values (i,e close to 1) mean non-significance. I don't know how
to do a power analysis with FDR.
On 11/19/18 1:16 PM, Laura Ferrero wrote:
> External Email - Use Caution
>
> Hi,
> I performed an statistical analysis comparing autism group with control group
> using volume/area an
On 11/19/18 7:34 AM, Crocetti, Deana wrote:
External Email - Use Caution
Hi Folks,
1) Can I derive a measure of extra-axial CSF. I realize this must be generated
in order to create the boundary between the skull and dura but not sure if this
is saved in as one of the labels.
Do you
I can' tell what is going wrong there. Can you run it with --debug as
the first option and send the output? BTW, the MC correction for LGI is
probably not very accurate. I would recommend using permutation. See
here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsCluster
On 11/16/18 7:34 PM, YAN Chao-Gan wrote:
External Email - Use Caution
Dear freesurfer experts,
I have a pretty naive question but would like to confirm.
When we use --3spaces option in multiple comparison correction, does that mean
we set the Cluster-wise threshold (cwp, not Cluster
, YAN Chao-Gan wrote:
External Email - Use Caution
Dear Douglas,
When doing --3spaces, is there a default subcortical mask in MNI space provided
by freesurfer? Where is it stored?
Thanks,
Chao-Gan
On Tue, Nov 20, 2018 at 10:12 AM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu
can you verify that /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
exists and that you have read permission to it? Eg, can you load it with
freeview -f /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
On 11/20/18 8:25 AM, C.P.E. Rollins wrote:
External Email - Use Caution
On 11/20/18 1:37 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
I had a question regarding the aseg.stats and was hoping to get some help.
1. How is the TotalGray calculated? On the wiki page it mentioned that it
is the sum of lhCortex + rhCortex + SubCortGray + Ce
did you put it in $FREESURFER_HOME/.license ? Is it world-readable?
On 11/20/18 2:38 PM, Sarah Haigh wrote:
> External Email - Use Caution
>
> Hello Freesurfers,
>
> Can anyone help with a licensing issue I have? I downloaded Freesurfer the
> other day with a brand new license and got th
No, it does not.
On 11/20/18 3:54 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Does the CerebralWhiteMatterVol (from the aseg.stats) include the cerebellum?
Thank you so much in advance for your help!
Best,
Da-yea
Disclaimer:
The materi
nal Compare CAU (0) And FCG (1)
> Class Main
> Variables group
> Input 005_long_pair Main 1
> Input 006_long_pair Main 0
>
> Thank you so much! I appreciate all your help with this!
>
> Best,
> Srishti
> Social/Clinical Research Specialist
&g
When you open it in freeview, you have to specify a surface (eg,
fsaverage/surf/lh.white) and then load that file as an overlay to that
surface
On 11/21/2018 05:11 PM, 姜时泽 wrote:
>
> External Email - Use Caution
>
> Dear freesurfer experts,
> I am using freesurfer to analyze my PET data
That looks ok. How did you create the FSGD file? Sometimes it can be a
little finicky about white space, and a file that looks ok might not
work (eg, if you made the file in windows). Can you send the actual FSGD
file as an attachement?
On 11/22/2018 09:09 AM, Larissa Bechtle wrote:
>
>
On 11/23/2018 11:26 AM, C.P.E. Rollins wrote:
> External Email - Use Caution
> Dear Freesurfer Developers,
> I have a 2-part question:
> 1) I was advised to use permutation to control for multiple
> comparisons in an LGI analysis, would you mind elaborating how to do
> this in command line (in
Use csdbase.y.ocn.dat
See
mri_glmfit-sim --help
for more info
On 11/24/2018 09:31 PM, Azeez, Azeezat wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I used FSGD option to run statistical test on 3 fixed factors each
> with 2 contrast levels. (DEVELOPMENT : old vs young, SEX: male
Can you send the fsgd file?
On 11/25/2018 10:44 AM, Damien MARIE wrote:
>
> External Email - Use Caution
>
> Hi,
> I would like to replicate an analysis I did with qdec but regressing out
> thickness at the vertex level. It’s a myelin group difference with age and
> left average myelin a
Try following this tutorial. It is for fmri, but you can probably apply
it to PET
surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview
Also see you PET module:
surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview
On 11/20/2018 06:34 PM, john Anderson wrot
L_cerebellum-cortex) + 52661.8
> (R_cerebellum-cortex) *= 750096.512392*
>
> There is still a difference of 1669.1. What could account for the
> difference?
>
> Best,
>
> Da-Yea
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh
fect of DEVxSEXxDIA shows decrease in cortical
> thickness at a specific cluster.
> Can this be interpreted to be "the localized cortical thickness
> decrease seen at cluster1 is a result of the interaction of DEVxSEXxDIA"
> Thank You
>
> On Mon, Nov 26, 2018 at 1:51 P
Do you have any scan that was acquired at the same time that is whole
head? Any scan will do. If so, you can run register-sess using the
-bbr-int option (or bbregister directly). Eg, if the anatomical was
acquired at the same time, then, to use register-sess, create a folder
in the session fold
le-head functional data.
>
> Il giorno lun 26 nov 2018 alle ore 22:07 Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>
> Do you have any scan that was acquired at the same time that is whole
> head? Any scan will do. If so, you can run regis
Sample the voxel-wise data onto the surface. Then use the --pvr
(per-vertex regressor) option in mri_glmfit. Search the mail archives
for more info.
On 11/20/2018 04:23 AM, Carola Mayer wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Developers,
>
> I have a general question
Yes, it can. You can also use mris_apply_reg, which is probably easier
to use. Run it with --help to get more info
On 11/29/2018 12:18 PM, 1013364183 wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Dear Bruce,
> ?0?2 ?0?2I want to know if mri_surf2surf can map high res
Use something like
mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf
beta.clusters.dat
See mri_glmfit-sim --help for more info on the OCN file and mri_segstats
--help for info on the avgwf file
On 11/29/2018 04:40 PM, Jahan, Bushra wrote:
> I am wondering how to extract beta values
Hi Matthieu, sorry for the delay
On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:
> External Email - Use Caution
>
> Dear Freesurfer's experts,
>
> I tried to use PETSurfer to correct partial volume effect on my FDG PET
> images, testing both Muller-Gartner and RBV corrections.
>
> I ra
You can use mri_annotation2label to extract a color table from the
annotation
On 12/03/2018 07:06 PM, Bruce Fischl wrote:
> Hi Stephanie
>
> can you give us some details about how you generated your fine-grained
> parcellation?
>
> cheers
> Bruce
> On Mon, 3 Dec 2018, Winkelbeiner, Stephanie A w
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas
> N.,Ph.D.
> Sent: Monday, December 03, 2018 7:11 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [EXTERNAL] Re: [Freesurfer] create ctab from annot
>
On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
>
> 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
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
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:
>
> External Email - Use Caution
>
> Hello,
>
> Is there a command to extract R
On 12/04/2018 02:17 PM, T and LS wrote:
>
> External Email - Use Caution
>
>
> 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:
>
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I am trying to
Can you send the full terminal output?
On 12/05/2018 01:25 AM, Sara Jafakesh wrote:
>
> External Email - Use Caution
>
>
>
>
>
>
> 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:
>
> External Email - Use Ca
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:
>
> External Email - Use Caution
>
> Dear experts,
> Is it necessary to install Matlab to use FsFast for functional
> connectivity?
> T
sorry, we don't have a hippo cortex analysis method
On 12/05/2018 10:26 AM, Yixin Ma wrote:
>
> External Email - Use Caution
>
> 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
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:
>
> External Email - Use Caution
>
> 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:
>
> External Email - Use Caution
>
> 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:
>
> External Email - Use Caution
>
> 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
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:
>
> External Email - Use Caution
>
> 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:
>
> External Email - Use Caution
>
> Hi everyone,
> thank you ver
On 11/27/2018 06:46 AM, C.P.E. Rollins wrote:
> External Email - Use Caution
> 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:
> External Email - Use Caution
>
> 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
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Greve,
> Douglas N.,Ph.D.
> *Sent:* Tuesday, November 20, 2018 6:22 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] CerebralWhiteMatterVol
>
> No, it does no
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:
>
> External Email - Use Caution
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:
>
> External Email - Use Caution
>
> 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:
>
> External Email - Use Caution
>
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:
>
> External Email
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
with --perm-force
>
>
> Can you please tell me how can I fix this issue or if I can run with
> --perm-force?
>
>
> Thanks for the help.
>
>
> On Thu, Dec 6, 2018 at 9:37 AM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> For
gt;
> 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.
>
> Thanks !
>
> On Thu, Dec 6,
On 12/06/2018 02:07 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> 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
Hi Lauri, what is non-ideal about it?
doug
On 12/06/2018 05:30 PM, Lauri Tuominen wrote:
> External Email - Use Caution
>
> 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
hi sara, can you include the entire email chain so that I can see the context?
On 12/7/18 4:19 PM, Sara Jafakesh wrote:
External Email - Use Caution
Dear Dr.GREVE ,
thank you for your reply
my full terminal outpou is :
[user@localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-se
look at subject/scripts/build-stamp.txt
On 12/7/18 5:09 PM, David Groppe wrote:
External Email - Use Caution
Hi FreeSurfers,
I'm working with some data that has been collected and processed with
FreeSurfer over several years. Consequently, some individuals have been
processed with
gt; Cc: dgr...@mgh.harvard.edu
> Date: Sat, 08 Dec 2018 22:25:20 +0330
> Subject: Fwd: fcseedcor output
>
>
> -Original Message-
> From: "Sara Jafakesh"
> To: "Greve, Douglas N.,Ph.D."
> Date: Sat, 08 Dec 2018
can you include previous emails so that we know what you are talking about?
On 12/11/18 7:15 AM, Maedeh Khalilian wrote:
External Email - Use Caution
Dear Bruce
The parcellation I have is not on surface, it is volumetric.
I wanna increase the number of its ROIs, I thought maybe I can cha
That all looks like it would work to me. Another thing you can try is the way
we create the wmparc.mgz using mri_aparc2aseg. You can find the commandline in
the recon-all.log file (make sure to set the output name so that you don't
overwrite wmparc.mgz). You can specify the max distance away fro
Sorry, the lGI code is not being maintained anymore
On 12/11/18 4:00 AM, Lorenzo Ferri wrote:
External Email - Use Caution
Dear expert
I am trying to calculate LGI for a subject. Now with some of your suggestions
it runs, but after one hour and half it gives me this errors
remeasuring
do you mean that nothing survived threshold? That happens sometimes.
On 12/10/18 8:03 AM, 1013364183 wrote:
External Email - Use Caution
Dear Bruce??
I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected
graphs are all 0. Why is this, the instructions and the run
The gamma and gammavar files are vertex-wise values. You can load them
in matlab with something like
g = MRIread('gamma.mgh');
gv = MRIread('gammavar.mgz');
but you will need the vertex that you are interested in (or do for all
vertices).
You can use fast_glm_power.m in the FSFAST toolbox to comp
That matrix will test for an effect of group regressing out the effect of age.
I would first test for an interaction between group and age with
0 0 0 1 -1 0
0 0 0 1 0 -1
Assuming that there is no effect, then I would re-run with DOSS
(different-offset, same-slope) with a contrast like
1 -1 0 0
1
That is not normal. Are you sure you are looking at the different maps that are
created?
Also, we are recommending that people not use MCZ (especially with such a low
threshold). Permutation is more accurate. See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm?high
Sorry, the disk that held that patch failed and we did not have a backup so not
everything was restored. I just put this file there:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
Copy it to $FREESURFER_HOME/bin. Let me know how it goes
On 12/10/18 12:4
d.edu] On Behalf Of Greve, Douglas
N.,Ph.D.
Sent: Tuesday, December 11, 2018 10:49 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than
vertices
External Email. Use Caution.
That all looks lik
not sure that you are trying to do. An annot is usually used for cortical
segmentation, not subcortical
On 12/9/18 5:57 PM, Conchy PF wrote:
External Email - Use Caution
Hello FS experts,
I was wondering if there is a command similar to annotval2surfoverlay.m that
allows converting su
> approach to read them the same?
> Thank you,
> Laura
>
>
>
>
>> El 11 dic 2018, a las 16:54, Greve, Douglas N.,Ph.D.
>> escribió:
>>
>> The gamma and gammavar files are vertex-wise values. You can load them
>> in matlab with something like
>
gt;
> Shall I use MRIRead & MRIWrite to change the values in aseg.mgz? How
> can I do it?
>
> Thank you and best regards,
>
> Conchy
>
> On Tue, Dec 11, 2018 at 4:18 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> not sure that yo
Yes, include the -T2pial flag
On 12/11/2018 12:06 PM, Maksimovskiy, Arkadiy wrote:
>
> Dear Experts,
>
>
> I am planning to run "recon" using T1 and T2 images, and was wondering
> if you wouldn't mind confirming whether this is the right command with
> recon:
>
>
> recon-all -s ${subject} -i T1.
Try lta_convert
On 12/11/2018 03:46 PM, Jane Tseng wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I was wondering if there is any way to convert the .dat file output
> from spmregister (generated using Freesurfer version 5.3) to a .lta
> file? Thank you!
>
> Be
--
> > matlab: Command not found.
> How can I fix it and obtain connectivity matrix with fcseedcor?
> thank you with your help ,
> sara
>
> -Original Message-
> From: "Greve, Douglas N.,Ph.D."
> To: Sara Jafakesh ,
> "freesurf
what do you mean by the white matter region? The aparc only labels
cortex, which is, of course, GM. If you mean the WM adjacent to the
aparc, have you looked at the wmparc.mgz file?
On 12/11/2018 05:16 PM, Song, Da-Yea wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I’ve been tryi
The FIR resolution is set with the TER parameter (-TER for mkanalysis).
You can try setting the TER to something shorter than the TR. This may
or may not work depending upon your jittering (it would have been
betterto have optseqed the stimuli with this in mind).
On 12/13/2018 12:23 PM, Lauri T
We don't have ways to automatically segment those (yet). They were
optimistically added to the LUT a few years ago:)
On 12/14/18 10:49 AM, Chama Belkhiria wrote:
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Dear comittee,
I need ROIs of Inferior Colliculus and Brainstem-cochlear-nucleus. Can
freesurfe
null)
>
> Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02
> UTC 2018 x86_64 x86_64
> x86_64 GNU/Linux
>
> Thanks
>
> Emanuel
>
>
> On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>>
urfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas
> N.,Ph.D.
> Sent: Tuesday, December 11, 2018 5:42 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Extracting both the GM and WM ROIs
>
> what do you
It could be anything related to the T1-weighting, so T1 itself or PD. It is
possible for the T2* to affect it, but usually the echo time is too short for
it to make much of a difference. I could imagine some other indirect effects
because of the normalization itself. The normMean was not added f
You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
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Hi Douglas,
Could you help me on this point ?
Best,
Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte
mailto:matthieuvanhou...@gmail.c
you can use mri_vol2surf to sample at different depths. If you want a simple
average across cortex, then you can use --projfrac-avg .35 .65 .05
If you want to do more sophisticated weighting, then you will have to sample at
each layer and then combine the files (eg, fscalc). Unless you have very
On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote:
> External Email - Use Caution
>
> Hi Douglas,
>
> Thanks for these clarifications. I added some others questions inline below.
>
> Best,
> Matthieu
>
>> Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D. a
There is not a way to get more decimals but you can apply a scaling
factor with --mul, eg, --mul 1000 will multiply the output by 1000
On 12/19/2018 04:01 PM, Winkelbeiner, Stephanie A wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer,
>
> Is there a way to print out more decimals
something like --meas white.K or white.H
On 12/19/2018 04:23 PM, Martin Juneja wrote:
>
> External Email - Use Caution
>
> Hi,
>
> Just like volume, I have "Folding Index" measures saved in
> lh/rh.aparc.stats files for each subject.
>
> If I am using mris_preproc *--meas volume* --out C
e tell me the difference between white.K and white.H
> conceptually and mathematically?
>
> On Wed, Dec 19, 2018 at 2:27 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> something like --meas white.K or white.H
>
>
> On 12/19/2018 04:23
The smoothing works through iterative nearest neighbor smoothing, so the
fwhm is essentially discretized because you can't have fractions of an
iteration. It looks like fwhm=0.66 is closer to 0 iterations than 1
iteration, so it chooses 0.
On 12/21/18 11:23 AM, sha...@nmr.mgh.harvard.edu wrot
No, not in the current framework. Even if there were, fwhm=.66 would not
give you much smoothing. The intervertex distance is about 1mm, at
fwhm=.66mm, the nearest vertex would be about 3 standard deviations
away, meaning that the smoothing would be minimal.
On 12/21/18 12:12 PM, sha...@nmr.mgh
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