Re: [Freesurfer] ASL processing in Freesurfer?

as Greve <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22> Mon, 21 Nov 2016 12:31:41 -0800 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20161121> No, not really. If you're not doing anything fancy

Re: [Freesurfer] ASL processing in Freesurfer? (Douglas Greve)

Many thanks for the information, Doug! I will give it a go. Actually, I would like to carry out the following analyses: Get regional estimates of perfusion within a region of interest as defined by a significant cluster after mri_glmfit-sim. as well as other cortical regions that are connected to

Re: [Freesurfer] Training Tracula to add more pathways

Hi Kris - The tracts have to be labeled manually in a set of subjects, that TRACULA uses as its training data. It takes the manually labeled tracts and the anatomical segmentation of each of the training subject and it computes the probability that a tract will go through or next to each segment

Re: [Freesurfer] [FreeSurfer] TRACULA Registration transform matrix

Hi Lauren - The transforms are all under dmri/xfms/... and the one you're looking for is the output of bbregister, which is called anatorig2diff.bbr.dat or .mat. Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on

Re: [Freesurfer] tracula reinit

Hi - It's not a requirement, but if the # of control points is specified for each tract, so if you've changed pathlist to a subset of the tracts, you have to do the same to the # of control points. The fewer control points the smoother the curve. More control points are more degrees of freedom.

Re: [Freesurfer] Getting combined bvals/bvecs

Hi Marisa - Is there by any chance the same file saved with 2 different extensions, like .nii and .nii.gz? I'd have to look at the entire trac-all.log to get a better idea when this happens. Thanks, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-b

Re: [Freesurfer] quality control of tracula tractography

Hi - See my answer to Knut Jørgen about the isosurfaces. I forgot to answer the second part of your question: the outliers of the -stat step are tracts that have a very different shape from the rest, so you can check those and see if they failed, but hopefully any QA/reinitialization would have

[Freesurfer] Fwd: recon-all -s Prueba2 exited with ERRORS

Hello FreeSurfer Developers, I'm attempting to compute autorecon1 and everything goes well until mri_nu_correct.mni, where I get the following error: /usr/local/freesurfer/subjects/Prueba2/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Martin, Thanks for replying. Please see inline below: > Le 21 nov. 2016 à 20:26, Martin Reuter a écrit : > > Hi Matthieu, > > a few quick answers. Maybe Jorge knows more. > Generally number of subjects / time points etc. cannot be specified > generally. All depends on how noisy your data

Re: [Freesurfer] Post recon anatomic file normalization

Hi Patrick we don't normalize into MNI coords. We compute the transform but process the images in their native space cheers Bruce On Mon, 21 Nov 2016, Bauer, Patrick M wrote: > Greetings, > > > I had quick question as to whether the final post-recon anatomical image (ie. > T1.mgz) retains the

[Freesurfer] Post recon anatomic file normalization

Greetings, I had quick question as to whether the final post-recon anatomical image (ie. T1.mgz) retains the normalization provided by the MNI template or if it is somehow reverted back to a pre-normalization format? Many thanks, Patrick Bauer PGY4 Neurology resident Medical College of Wi

Re: [Freesurfer] ASL processing in Freesurfer?

No, not really. If you're not doing anything fancy (eg, just computing mean of tag-control) and mapping to the surface, it is easy enough to do (mri_concat --paired-diff --sum, then bbregister to register to the anat, then mri_vol2surf or mris_preproc to map to fsaverage, then mri_glmfit and mr

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Matthieu, a few quick answers. Maybe Jorge knows more. Generally number of subjects / time points etc. cannot be specified generally. All depends on how noisy your data is and how large the effect is that you expect to detect. You can do a power analysis in order to figure out how many sub

Re: [Freesurfer] Mris_decimate for MAC

HI Zake, Yes the binary from the link doesn't work, but I have downloaded the newest version and it there. Thanks Dorothy On Mon, Nov 21, 2016 at 7:06 AM, Z K wrote: > Hello Dorothy, > > I have reenabled the link below. However, there is a very high > likelihood that this mris_decimate binary

Re: [Freesurfer] trouble with mailing list

Hello, I've looked into this issue some and it appears the issue is with emails that contain "large" image attachments. We generally approve emails which contain attachments that exceed the attachment size limit, but mail-archive.com has their own policy on the matter. Please see the following

Re: [Freesurfer] trouble with mailing list

Im subscribed to the list and I see your messages with the jpgs. The header info is pasted below. Some users messages (including yours) are not showing up on the mail-archives site, but they are being sent out to the list. Did you not receive the messages you sent out? Forwarded M

[Freesurfer] ASL processing in Freesurfer?

Hi Freesurfer Team, Is there an ASL-friendly processing pipeline embedded in Freesurfer? Something like an equivalent to that of PetSurfer? Thanks. Best Wishes, Elijah Sent from my iPad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] trouble with mailing list

Are there trouble with messages that contains attachments like jpgs? I have sent two questions with pictures that I have received post acknowledgment, but they do no appear in the mailing list. Thanks Knut Jørgen On 21 Nov 2016, at 17:34, Z K mailto:zkauf...@nmr.mgh.harvard.edu>> wrote: Thi

Re: [Freesurfer] Help with Opseq: Setting Parameters

Not really. You can force there to always be a NULL with --tnullmin. You can also specify the maximum duration of the null event with --tnullmax; this should indirectly cause there to be more instances where nulls appear between non-nulls. On 11/21/16 1:17 PM, Leshin, Joseph wrote: Greeting

[Freesurfer] Help with Opseq: Setting Parameters

Greetings, Is it possible to avoid having Optseq repeat my events more than 3 times before inserting a NULL? In other words, I get sequences that look like ev1, ev5, ev4, ev2, ev6, NULL, etc. Ideally, I'd have Optseq limit event repetitions at 2-3 followed by a NULL. I tried using "-repvar" bu

[Freesurfer] Longitudinal stream : LME and limits of model

Dear Freesurfer’s experts, I would have some questions regarding the LME model to be used in longitudinal stream: 1) Which are the ratio limits or % of missing timepoints accepted ? (according time, I have less and less subjects time points) 2) Is it possible to include patients that would mis

[Freesurfer] Tenure track position in Biomedical Imaging Science at Harvard (fwd)

FYI -- Forwarded message -- Date: Mon, 21 Nov 2016 10:45:52 -0500 From: Hanspeter Pfister To: Bruce Fischl , Bruce Rosen Subject: Tenure track position in Biomedical Imaging Science at Harvard Hi Bruce and Bruce, I hope all is well. I would appreciate if you could distri

Re: [Freesurfer] trouble with mailing list

This seems to be an issue as there are other recently confirmed cases of emails missing from the archive. In these instances, messages are distributed to the freesurfer support list, but do not show up on the mail-archives.com website. We will look into the matter but it appears to be more of a

[Freesurfer] trouble with mailing list

Hi I have posted two posts to the FreeSurfer mailing list that does not appear in the archive. Are there any trouble with the list or are there a trouble with my mailing client? Knut Jørgen Bjuland PhD ___ Freesurfer mailing list Freesurfer@nmr.mgh.

[Freesurfer] Error w/ recon-all

Hello FreeSurfer Developers, I’m trying to run recon-all on a cluster of images, however I keep getting an error each time. Here’s the output and command line: [jawilks@tykwer subjects]$ recon-all -subjid run_02 -all Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp:

Re: [Freesurfer] grayscale display turns red in freeview

Ok. Will try to run it locally. thanks On Mon, Nov 21, 2016 at 5:00 PM, Ruopeng Wang wrote: > This is likely due to remote display. Would it be possible for you to run > it locally? You can also adjust overlay settings from the command-line, > although it is not as convenient as the GUI. Run “fr

Re: [Freesurfer] grayscale display turns red in freeview

This is likely due to remote display. Would it be possible for you to run it locally? You can also adjust overlay settings from the command-line, although it is not as convenient as the GUI. Run “freeview -h” and look for surface overlay related options. > On Nov 21, 2016, at 9:48 AM, Emmanuel

Re: [Freesurfer] Mris_decimate for MAC

Hello Dorothy, I have reenabled the link below. However, there is a very high likelihood that this mris_decimate binary will not work with your version of freesurfer. This is because the Mac version of freesurfer has changed significantly since its release 3.5 years ago. However, the mris_deci

Re: [Freesurfer] grayscale display turns red in freeview

Can you post a screenshot? Are you running freeview remotely? > On Nov 21, 2016, at 9:32 AM, Emmanuel Nwosu > wrote: > > it opens a blank "configure overlay" dialog, then the screen goes dark > > On Mon, Nov 21, 2016 at 4:29 PM, Ruopeng Wang > wrote: > What

Re: [Freesurfer] grayscale display turns red in freeview

it opens a blank "configure overlay" dialog, then the screen goes dark On Mon, Nov 21, 2016 at 4:29 PM, Ruopeng Wang wrote: > What happens when you click on the button? > > On Nov 21, 2016, at 9:02 AM, Emmanuel Nwosu > wrote: > > Thanks Ruopeng. I can't open the configure overlay button. Is the

Re: [Freesurfer] Problem checking out sources

Hello, We are phasing out the cvs repository and transitioning to git. You may find this page useful: http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page -Zeke On 11/21/2016 06:30 AM, Marmaduke Woodman wrote: > hi > > I followed the instructions for checking out the so

Re: [Freesurfer] grayscale display turns red in freeview

What happens when you click on the button? > On Nov 21, 2016, at 9:02 AM, Emmanuel Nwosu > wrote: > > Thanks Ruopeng. I can't open the configure overlay button. Is there any other > means of changing it? > > On Mon, Nov 21, 2016 at 3:58 PM, Ruopeng Wang >

Re: [Freesurfer] Mris_decimate for MAC

Hi Zake Actually, it was you in one of the emails who linked a version for MAC: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37701.html Then, Doug also posted a link for mri_decimate for MAC: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg44192.html Is it possible

Re: [Freesurfer] grayscale display turns red in freeview

Thanks Ruopeng. I can't open the configure overlay button. Is there any other means of changing it? On Mon, Nov 21, 2016 at 3:58 PM, Ruopeng Wang wrote: > You need to adjust the color scale. Click on “Configure Overlay” button to > adjust it. > > Best, > Ruopeng > > On Nov 21, 2016, at 3:52 AM,

Re: [Freesurfer] Importance of Symbolic Links?

Thank you for the info. It definitely puts some ease on my situation. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: Sunday, November 20, 2016 9:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [

Re: [Freesurfer] grayscale display turns red in freeview

You need to adjust the color scale. Click on “Configure Overlay” button to adjust it. Best, Ruopeng > On Nov 21, 2016, at 3:52 AM, Emmanuel Nwosu > wrote: > > Hi > > Am having a bit of a problem that may be easy to resolve. > > I want to view an LGI two-group comparison I did in mri glm-fit

[Freesurfer] Problem checking out sources

hi I followed the instructions for checking out the sources, by logging in first and then trying to checkout ~/src/fs$ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot co -P -r stable5 dev cvs server: cannot find module `dev' - ignored cvs [checkout aborted]: cannot expand module

[Freesurfer] Fwd:

Hi Am having a bit of a problem that may be easy to resolve. I want to view an LGI two-group comparison I did in mri glm-fit with freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mgh). The grayscale inflated surface turns red like what is in picture-1 Please have anyone an idea

[Freesurfer] grayscale display turns red in freeview

Hi Am having a bit of a problem that may be easy to resolve. I want to view an LGI two-group comparison I did in mri glm-fit with freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mgh). The grayscale inflated surface turns red like what is in picture-1 Please have anyone an idea