Re: [Freesurfer] T2pial shrinks pial surface

Thanks Bruce, Doing the bias correct and -odt float fixed the issue. Adding -odt short did not. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, 8 March 2016 11:46 AM To: Freesurfer

[Freesurfer] Position at UW (fwd)

FYI -- Forwarded message -- Date: Tue, 8 Mar 2016 02:00:35 + From: THOMAS J. GRABOWSKI To: Bruce Fischl Subject: Position at UW Hi Bruce, I am looking for a research scientist with expertise in fMRI experimental design and

Re: [Freesurfer] Medial crossing surfaces

Hi Bruce,Thanks, I uploaded my subject in your ftp site.case name: train_emc_010.tar.gz Best,Maryam   On Monday, March 7, 2016 5:26 AM, Bruce Fischl wrote: Hi Maryam I guess, although it's hard to say without looking at your data. I think the

Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

On 7 March 2016 at 11:25, Francis Tyson Thomas wrote: > That information was a lot helpful. At this point I'm currently trying to > reduce the recon-all processing time as much as possible and for this reason > I was looking to get the -use-gpu flag working. I'm

Re: [Freesurfer] T2pial shrinks pial surface

it might, but you will need to make some fixes that are in 6.0 (soon) but not in 5.3. The 5.3 recon-all changes the T2 datatype to uchar when it resamples it to be in register with the T1. You should change that line to have -odt short or -odt float so that it doesn't saturate at 255, which is

Re: [Freesurfer] T2pial shrinks pial surface

I see it now. I will try to perform a bias correction on the image prior to importing and see if that helps. Thanks Bruce. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, 8 March

Re: [Freesurfer] Cortical thickness using freesurfer

is this still a problem? On 03/04/2016 01:24 PM, Sahil Bajaj wrote: > Dear all, > > I am working on calculation of cortical thickness from a set of > subjects. I am following the instructions from > https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and > I am able to run

Re: [Freesurfer] error - mri_nu_correct.mni

what happens when you run the following? cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz On 03/07/2016 04:09 PM, Flavia Niccolini new wrote: > Hello, > > I was wondering whether

Re: [Freesurfer] mris_anatomical_stats -th3

/*! \fn MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol) \brief Compute vertex-wise volume based on dividing each obliquely truncated trilateral pyramid into three tetrahedra. Based on Anderson M. Winkler's srf2vol matlab script. \params w is white surface, p is pial. Output is an MRI

Re: [Freesurfer] group analysis all measures same results

what are your command lines? On 03/04/2016 09:01 PM, Kaiming Yin wrote: > Dear guys, > > I was doing group analysis (command-line) on two groups (patients and > control, no age or other information). The data has been "qcached", > and after following the three steps as "mris_preproc, mri_glmfit

Re: [Freesurfer] Cortical thickness last step

The code that does this is hard-coded and hard for me to follow (eventhough I wrote it:). It might be faster to to try to change ROI5.mgh. How did you create */media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh?* On 03/04/2016 04:31 PM, Sahil Bajaj wrote: > > Hello again, > > > To calculate

Re: [Freesurfer] mean thickness

the table file lh.aparc.thickness.table should be an ascii file. when you look at it with cat/more/less, what do you see? Can you send that table file? On 03/07/2016 04:33 AM, Caroline Beelen wrote: > Hi Bruce, > > I'm a beginner in FS, so I just followed tutorial instructions for generating

Re: [Freesurfer] Embed vol geom in surf file

It isn't recognized: $ mris_convert --vol-geom mri/T1.mgz ../fsaverage5/surf/lh.pial.tvb.bad surf/lh.pial.bad unknown option --vol-geom I can stick with the dev version if no command line utility is available for this in the stable version. De :

Re: [Freesurfer] recon-all issues

Are you sure the job was not killed in the middle? The recon-all.log file just stops without a warning or error message. Or does this happen repeatedly? On 03/07/2016 03:10 PM, Julian Jäckle wrote: > Thank you so much for the response. Unfortunately I am not so familiar > with freesurfer but

Re: [Freesurfer] Embed vol geom in surf file

I mean that the mri_surface structure and the file format it uses both allow a vox2ras transform to be stored. I guess the matlab code doesn't support it, but it could be modified to do so if anyone was interested Bruce On Mon, 7 Mar 2016, WOODMAN Michael wrote: > sorry to bother, but can you

Re: [Freesurfer] Embed vol geom in surf file

sorry to bother, but can you elaborate? mris_convert --help doesn't show anything. De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Bruce Fischl the surface files do support

[Freesurfer] error - mri_nu_correct.mni

Hello, I was wondering whether you could help with this error: # #@# MotionCor Thu Mar 3 11:35:51 GMT 2016 Found 1 runs /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only

Re: [Freesurfer] TRACULA messy tracts

Dear Anastasia, Thank you! Wouldn't you mind for example sending me these tables? As far as I am concerned I need only one table for all my subjects, so that would help me a lot. The issue with flipped coordinates in the gradient table is, as I mentioned before, due to the fact that I obtained

Re: [Freesurfer] recon-all issues

Thank you so much for the response. Unfortunately I am not so familiar with freesurfer but these files do not exist: transforms/talairach_with_skull.lta, brainmask.auto.mgz, brainmask.mgz. I don’t know if it is helpful but below I listed all files which can be found in the subjects directory

Re: [Freesurfer] Embed vol geom in surf file

On 03/07/2016 08:34 PM, dgw wrote: > Marmaduke, > > Could you describe what it is you want to do? What do you mean by > volume geometry? What type of information do you want to put on the > surface? I wish to approximate the effect of the --tval-xyz vol argument to mris_surf2surf in the dev

Re: [Freesurfer] Embed vol geom in surf file

the surface files do support embedding a ras2vox transform in them On Mon, 7 Mar 2016, dgw wrote: > Marmaduke, > > Could you describe what it is you want to do? What do you mean by > volume geometry? What type of information do you want to put on the > surface? > > d > > On Mon, Mar 7, 2016 at

Re: [Freesurfer] Embed vol geom in surf file

Marmaduke, Could you describe what it is you want to do? What do you mean by volume geometry? What type of information do you want to put on the surface? d On Mon, Mar 7, 2016 at 2:31 PM, marmaduke woodman wrote: > hi > > Is it possible to embed a volume geometry

[Freesurfer] Embed vol geom in surf file

hi Is it possible to embed a volume geometry in a surface file explicitly? I'm unable to find a mri_ or mris_ command which seems to do this. Is there any workaround via the GUI tools? Thanks, Marmaduke ___ Freesurfer mailing list

Re: [Freesurfer] recon-all issues

Hi Julian can you give us more details about what exactly is missing? cheers Bruce On Mon, 7 Mar 2016, Julian Jäckle wrote: Dear FS-team For purposes of measuring cortical thickness I’ve been running recon-all as described on your RecommendedReconstruction site. However I am missing

[Freesurfer] recon-all issues

Dear FS-team For purposes of measuring cortical thickness I’ve been running recon-all as described on your RecommendedReconstruction site. However I am missing some files including e.g the skullstripped file. Could you check my log file for the root cause? Greetings Julian recon-all.log

Re: [Freesurfer] Tracula bedpostx error

Hi Prad - I'm guessing the tutorial was generated with an earlier version of bedpostx, tracula, or a combination of both. So I wouldn't expect to find the exact same values. As long as things run and the files are generated, it looks like you're fine. Best, a.y On Mon, 7 Mar 2016,

Re: [Freesurfer] Tracula bedpostx error

Hi Anastasia, Thank you for clarifying that. I have a follow up question. To avoid this error while running the ball and stick model fit( Syntax error: "(" unexpected), I ran it locally using "bedpostx $path_to_dmri". The results of the overall path statistics differ from those in the

Re: [Freesurfer] path.pd.trk format

Anatorig will take you to freesurfer space. I's suggest smoothing these to make them more presentable, and potentially also thresholding them based on the probability map (which is the sum of these streamlines). On Mon, 7 Mar 2016, Peled, Noam wrote: > I want to display it in my new 3d

Re: [Freesurfer] path.pd.trk format

I want to display it in my new 3d visualization tool, along the hemispheres and the subcortical regions. The hemispheres and the subcortical regions I import from freesurfer. Thanks, Noam From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] T2pial shrinks pial surface

Hi Chris I took a look, and the problem is that there are big changes in contrast between occipital and frontal lobes. If we normalize both posterior and frontal wm to 110, occipital gray matter gets mapped to 180 but frontal gray gets >255. This kind of thing can be caused by a transmit

Re: [Freesurfer] path.pd.trk format

What to you want to display it on? If you want to display in on the FA map, or anything that's in diffusion space, you don't need any transform. On Mon, 7 Mar 2016, Peled, Noam wrote: > So for plotting the fibers, like in freeview, should I just use the > /dmri/xfms/diff2anatorig..mat or >

Re: [Freesurfer] Tracula bedpostx error

Hi Prad - What will affect the speed is whether you run it locally on your computer (in which case it'll process one slice after the other) or on a cluster (in which case all the slices will be processed in parallel on different nodes of the cluster). This is the case regardless of the

Re: [Freesurfer] path.pd.trk format

So for plotting the fibers, like in freeview, should I just use the /dmri/xfms/diff2anatorig..mat or /dmri/xfms/diff2anat..mat transformation matrices? Thanks again, Noam From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] path.pd.trk format

Yes, native diffusion space. On Mon, 7 Mar 2016, Peled, Noam wrote: > Thanks! > Do you in which space are the voxel coordinates coordinates? Are they in the > diffusion space? > > Thanks again, > Noam > > From: freesurfer-boun...@nmr.mgh.harvard.edu >

Re: [Freesurfer] TRACULA messy tracts

Hi Jacek - I looked at the data that you uploaded. The problem is that both the b-value table and the gradient table that you were using were assuming that the b=0 images were interspersed throughout your scan, when in fact based on your dicoms they are all in the begining of the scan. So

Re: [Freesurfer] Recon Reprocessing Issues

I got it, thanks Bruce On Mon, 7 Mar 2016, Champe Barton wrote: Hey Bruce, I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend

Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

Hi Richard, That information was a lot helpful. At this point I'm currently trying to reduce the recon-all processing time as much as possible and for this reason I was looking to get the -use-gpu flag working. I'm currently running a freesurfer v6 beta version on Ubuntu 14.04.4. With regard to

Re: [Freesurfer] Recon Reprocessing Issues

Hey Bruce, I got a notification saying the email my recon-all.log file attachment was too large and had to await moderator approval to be posted to the support list. I was just wondering if you received it or if I should resend it. Best, Champe Sent from my iPhone > On Mar 6, 2016, at 9:53

[Freesurfer] Hiring: Houston, TX - Data Processing/Analysis

Hello, The Nantz National Alzheimer Center, in Houston, TX is looking to fill two positions pertaining to neuroimaging and analysis. Be aware that we cannot accept remote employment, the candidate would have to work day-to-day in the city of Houston. Any interested person is encouraged to

Re: [Freesurfer] path.pd.trk format

Thanks! Do you in which space are the voxel coordinates coordinates? Are they in the diffusion space? Thanks again, Noam From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki

[Freesurfer] mri_convert Ubuntu 14.04 LTS not working (neither is freeview)

Dear all, I have just installed FreeSurfer 5.3.0. on Ubuntu 14.04 LTS (64-bit). The mri_convert doesn't work with no error message. which mri_convert gives /usr/local/freesurfer/bin/mri_convert. Of course neither does recon-all (which exits with errors with no error message in the log). I

Re: [Freesurfer] Medial crossing surfaces

Hi Maryam I guess, although it's hard to say without looking at your data. I think the upcoming V6 does much better on the midline. If you upload your data I can take a look. For the command line you can check out the recon-all help and just rerun the pial surface generation cheers Bruce On

[Freesurfer] System crash by extremely much generated output v6 beta

Hi developers, My environment: MacPro OSX10.7 installed on a partition of 20 GByte; FreeSurfer v6 beta During processing recon-all on 4 subjects in parallel using 4 terminal windows, the 20 GByte partition got full. This happened twice and I managed to trace down the offending stage in the

[Freesurfer] Medial crossing surfaces

 Hi Bruce,I am editing aseg to correct the boundaries that excluded the lateral ventricle. The problem with lateral ventricle has been solved after running the process with -noaseg flag. But the boundaries in the middle, is crossing to the other hemesphere in some cases. I even tried