Re: [Freesurfer] undo pial edits only

Hi Bruce, thanks for your quick reply. No I am editing using the following command: tkmedit PARTICIPANT_FOLDER wm.mgz rh.white -aux brainmask.mgz -aux-surface lh.white Thanks, Torsten On Mon, 2011-10-03 at 11:22 -0400, Bruce Fischl wrote: > what pial edits to you want to undo specifically? Was

[Freesurfer] FreeSurfer Compiling error

Hi FreeSurfers, I'm trying to compile freesurfer with --enable-fermi-gpu and cuda 4. The process stopped with this error message: make[3]: Entering directory `/home/neuro/dev/mri_em_register' /usr/local/cuda/bin/nvcc -o em_register_cuda.o -c em_register_cuda.cu -arch sm_20 --ptxas-options=-v -g -

Re: [Freesurfer] Automatic correct of mislabeling around ctx- lateral orbital?

Hi Knut, in part it depends on the bandwidth and readout direction of your acquisition, as with the wrong parameters orbital fat can shift into brain and then there is really nothing you can do to recover the true anatomy in that location. Can you send us an image? thanks Bruce On Tue, 4 O

Re: [Freesurfer] undo pial edits only

and which volume are you editing? On Tue, 4 Oct 2011, Torsten Ruest wrote: > Hi Bruce, > > thanks for your quick reply. No I am editing using the following > command: > > tkmedit PARTICIPANT_FOLDER wm.mgz rh.white -aux brainmask.mgz > -aux-surface lh.white > > Thanks, > > Torsten > > On Mon, 2011-

Re: [Freesurfer] FreeSurfer Compiling error

On Tue, Oct 4, 2011 at 5:06 AM, Jordi Delgado wrote: > I'm trying to compile freesurfer with --enable-fermi-gpu and cuda 4. The > process stopped with this error message: I'm not certain, but I believe CUDA 4 has thrust included. This might conflict with the version installed in the source tree.

Re: [Freesurfer] undo pial edits only

to correct the pial surface for incorrect assignment of head tissue, I edit the brainmask.mgz. Hope that's correct... Thanks, Torsten On Tue, 2011-10-04 at 09:07 -0400, Bruce Fischl wrote: > and which volume are you editing? > On Tue, 4 Oct 2011, Torsten Ruest wrote: > > > Hi Bruce, > > > > tha

Re: [Freesurfer] undo pial edits only

Hi Torsten, If you run: recon-all -all -clean-bm -s subjid This should trask all the edits you made to the brainmask volume and make a new one to replace that. It will keep all your other edits. Allison On Tue, 4 Oct 2011, Torsten Ruest wrote: > to correct the pial surface for incorrect assignm

Re: [Freesurfer] undo pial edits only

Thanks Allison, that's great! Torsten On Tue, 2011-10-04 at 09:40 -0400, Allison Stevens wrote: > Hi Torsten, > If you run: > recon-all -all -clean-bm -s subjid > > This should trask all the edits you made to the brainmask volume and make > a new one to replace that. It will keep all your other

[Freesurfer] tkmedit window size

Hi there, I was wondering whether there is better option to resize the tkmedit window: when I drag it bigger, it appears that the same change in aspect ratio is applied to the image I am working on. When using the zoom option (x2), the image I am working on doesn't fit completely into the window a

Re: [Freesurfer] tkmedit window size

Hi Torsten, I believe we have this on our to do list for tkmedit fixes. Allison On Tue, 4 Oct 2011, Torsten Ruest wrote: > Hi there, > > I was wondering whether there is better option to resize the tkmedit > window: when I drag it bigger, it appears that the same change in aspect > ratio is app

Re: [Freesurfer] tkmedit window size

no, sorry. Why not zoom first, then drag to make it bigger? On Tue, 4 Oct 2011, Torsten Ruest wrote: > Hi there, > > I was wondering whether there is better option to resize the tkmedit > window: when I drag it bigger, it appears that the same change in aspect > ratio is applied to the image I am

Re: [Freesurfer] (no subject)

Hi Heather, The cerebellum is not included in 5.1's total subcortical gm or total gm volumes. Let me double check on what is included in the subcortical gray matter total volume. Allison On Mon, 3 Oct 2011, Lugar, Heather wrote: > Can you please tell me if the cerebellum is included in Freesurf

Re: [Freesurfer] tkmedit window size

Hi, I don't think the order of zooming and dragging matters, it appears that the result is the same: I cannot drag the window independently of the image, this will change in size as well... Thanks, Torsten On Tue, 2011-10-04 at 09:50 -0400, Bruce Fischl wrote: > no, sorry. Why not zoom first,

[Freesurfer] cuda error...

Hi: I installed CUDA 4 in a Ubuntu 10.10 based workstation... I tried to process a volume, but I got the following error: "writing output transformation to transforms/talairach_with_skull.lta... CUDA Error in file 'gcasgpu.cu' on line 159 : unspecified driver error. registration took 15 minutes

[Freesurfer] cwp and QDEC color scale

Hello Surfers, I would appreciate if you can help me with the following question: what should be the range values on the  QDEC and/or GLM  color scale if the cwp values for the cached clusters at thresh 2 and cwpvalthresh .99 are between 0.4465 and 0.9710? Many thanks. AK__

Re: [Freesurfer] cuda error...

On Tue, Oct 4, 2011 at 11:15 AM, Gonzalo Rojas Costa wrote: >  I installed CUDA 4 in a Ubuntu 10.10 based workstation... I tried to > process a volume, but I got the following error: > > "writing output transformation to transforms/talairach_with_skull.lta... > CUDA Error in file 'gcasgpu.cu' on

[Freesurfer] cwp and QDEC color scale

Hello Surfers, I would appreciate if you can help me with the following question: what should be the range values on the  QDEC and/or GLM  color scale if the cwp values for the cached clusters at thresh 2 and cwpvalthresh .99 are between 0.4465 and 0.9710? Many thanks. AK__

Re: [Freesurfer] Dimension Mismatch Error

Hi Doug and Freesurfers, No matter what I try I am still getting the Dimension mismatch error when running fieldsign-sess. I even ran recon-all -s sj12 -make all. I don't think it's a problem with the directories (below). The subjectname file is correct, and when I run field-sign-sess it sees th

Re: [Freesurfer] Dimension Mismatch Error

Hi Michell, you appear to have two FreeSurfer analysis for this subject: /usr/local/freesurfer/subjects/ld12 /usr/local/freesurfer/subjects/retinotopy/sj12 Can you verify that these are *exactly* the same? doug Michelle Umali wrote: > Hi Doug and Freesurfers, > No matter what I try I am still

[Freesurfer] funcroi-table-sess with multiple contrasts

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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

Re: [Freesurfer] funcroi-table-sess with multiple contrasts

sorry, only one contrast doug SHAHIN NASR wrote: > 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 > -- Douglas N. Greve

[Freesurfer] upload issues for file drop

hi Freesurfers, I am trying to upload a 1.4 GB tgz file and I can't register as a new user through Accellion File Transfer. When I try uploading through regular File Drop, the connection times out (because the file is too big?). How can I upload this file? Thanks. Michelle __

Re: [Freesurfer] upload issues for file drop

Try this Sharing Data with non-Martinos users In order to receive files from remote users who do not have center accounts, one must have them use the /anonymous/ ftp server surfer.nmr.mgh.harvard.edu. For remote users to upload files, they should connect to ftp://surfer.nmr.mgh.harvard.e

[Freesurfer] .img unsupported data type ?

Dear FreeSurfers, First of all, I am completely new to FS so forgive me if I missed something simple. I am currently running freesurfer v5.1.0, using the .vdi file with VirtualBox. (Host = windows 7). I tested the program by running the autorecon1 on subject "bert" and everything seems to work