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Hi Greve,
Thank you very much for your reply.
How do I add data to the link you sent me? When I click on it, a pop up
appears and I need to fill in a password to connect to the server. Which
password should I use?
If I copy the link on a browser,
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Dear Freesurfer experts,
I am currently trying to use mri_vol2surf on my bold data. I typed this
commandline :
"
mri_vol2surf --mov
${dir1}/${subject}/${subject}${scan}_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
\
--mni152reg \
-
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Hello FreeSurfer Developers,
I am having trouble opening the updated version of Freeview. I have
followed the directions for Linux on the UpdateFreeview site (
http://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview), but when I get to
the last step an
Hi Ileana
you use "anonymous" for the user name and your email for the password I
believe.
cheers
Bruce
On Wed, 17 Apr 2019, Camerino, .I.L. (Ileana) wrote:
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Hi Greve,
Thank you very much for your reply.
How do I add data to the link you sent me? When I
can you send the full terminal output of the mri_surf2vol command?
On 4/17/19 5:59 AM, Loïc Daumail wrote:
>
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>
> Dear Freesurfer experts,
>
> I am currently trying to use mri_vol2surf on my bold data. I typed
> this commandline :
> "
> mri_vol2surf --mov
>
Sorry, I've been having problems getting the patch together because of
difficulties compiling version 6 on centos 7. Should be ready today.
On 4/16/19 11:43 PM, Alvarado,Luis R wrote:
>
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>
> Dear Freesurfers,
>
> I just read the page about “Fixing of Morphome
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Postdoctoral Opportunity at Mass General Hospital –
Harvard Medical School
The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at
Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in
Boston, Massachusett
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Dear Doug Greve,
Sorry, issue solved!
I had used a wrong path directory in the commandline... it’s now working
perfectly well.
Thanks for your help,
Sincerely,
Loïc Daumail
Le mer. 17 avr. 2019 à 17:25, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.e
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Douglas,
Thank you for working on the patch. I didn’t mean to rush you or anything. I
was just wondering if I was missing something.
Thank you,
Luis R. Alvarado
On 4/17/19, 11:26 AM, "Greve, Douglas N.,Ph.D." wrote:
Sorry, I've been having
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Hi Bruce,
I dragged into the folder "incoming" a folder called "sub025" (soft failure)
for the first problem and a folder called "sub-31" (hard failure) for the
second problem
Can you see them?
Thanks
Looking forward to hear from you
Ileana
Ilean
can you be more specific?
On 4/17/19 12:20 PM, Alvarado,Luis R wrote:
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>
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_
The patch is there now, try it. It is likely that it does not affect you
unless you are using high-res data.
On 4/17/19 12:30 PM, Alvarado,Luis R wrote:
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>
> Douglas,
>
> Thank you for working on the patch. I didn’t mean to rush you or anything. I
> was jus
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Hello Kelly,
Do you have libfreetype installed on your system (which defines that symbol)?
$ strings /usr/lib64/libfreetype.so.6 | grep -i ft_get_font_format
FT_Get_Font_Format
If not, you can install it with,
$ sudo yum install freetype.x86_64 freetyp
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Thank you for your help!
When I look within /usr/lib64 (using ls *libfreetype*) , I see:
lib64/libfreetype.so.6 lib64/libfreetype.so.6.10.0
When I type:
strings /usr/lib64/libfreetype.so.6 | grep -i ft_get_font_format
I do not get any output.
When I
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mri_glmfit --y lh.t1t2ratio_12CMT_fmed_3sm_decurv.fsavg.mgh --fsgd
age_dexterity.fsgd --surf fsaverage lh --C contrast.mtx --o
lh_NHPT_T1T2_12CMT_allbrain
Il giorno gio 11 apr 2019 alle ore 21:58 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> ha sc
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Please disregard this last email. I was trying to make adjustments to my mail
list settings by following these instructions from the welcome email:
You can also make such adjustments via email by sending a message to:
freesurfer-requ...@nmr.mgh.ha
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Hi Doug,
After some false starts, I may have uploaded CM_f.nii.gz to the
/transfer/incoming folder (my ftp client reports the upload was complete, but
the directory listing afterwards shows 0 files).
In the event that my ftp client lied to me about t
can you send your fsgd file and your contrast.mtx file?
On 4/17/19 4:12 PM, TMS lab wrote:
>
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>
>
> mri_glmfit --y lh.t1t2ratio_12CMT_fmed_3sm_decurv.fsavg.mgh --fsgd
> age_dexterity.fsgd --surf fsaverage lh --C contrast.mtx --o
> lh_NHPT_T1T2_12CMT_allbrain
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There you go.
The contrast.mtx gives me the error
ERROR: dimension mismatch between X and contrast contrast.mtxX has 3
cols, C has 4 cols
Il giorno mer 17 apr 2019 alle ore 22:12 TMS lab ha
scritto:
>
> mri_glmfit --y lh.t1t2ratio_12CMT_fmed_3sm
I was able to get it from the ftp, but I was not able to replicate the
error. The last 70 or so time points of this data set are all 0s. I
don't think this was the problem, but it might have been. In any event,
it will mess up everything else unless you've used time point exclusion
files. You c
In this case, there is only one class and two continuous variables, so
there will be only 3 regressors, so your contrast matrix should only
have 3 items. try 0 0 1
On 4/17/19 5:17 PM, TMS lab wrote:
>
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>
> There you go.
> The contrast.mtx gives me the error
label2vol is probalby a little more accurate
On 4/16/19 7:47 PM, Sam W. wrote:
>
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>
> Thank you Douglas. So that means I can basically use either one for
> freesurfer to native space conversion, is that right? Is there any
> case in which label2vol should de
If you want to transfer a segmentation, then it is better to use
mri_label2vol with the --seg option. Run it with --help to get examples.
Probably even better is to transfer your functional to anatomical space
(mri_vol2vol) so that it is in registration with the anatomical;
transferring it to a
Use mri_label2vol with --fill-ribbon. Note that you can use this to
convert the aparc.a2009s into the volume space, then use something like
mri_binarize to extract the labels you want.
On 4/16/19 7:52 PM, Sam W. wrote:
>
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>
> Hi,
> I created a series of labe
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