Re: [Freesurfer] Any updates on recon-all GPU support?

Hi Richard, Fixed the gcc problems as well (this required a tweak to host_config.h in /usr/local/cuda/include). Now, I've hit another roadblock: Makefile:4542: recipe for target 'libutils_cuda_a-mrisurf.o' failed make[3]: *** [libutils_cuda_a-mrisurf.o] Error 1 make[3]: *** Waiting for

Re: [Freesurfer] Any updates on recon-all GPU support?

On 23 June 2016 at 16:26, Derek Pisner wrote: > Hi Richard, > > Hope this finds you well. I followed your instructions and compiled from > source (you were right-- compiling Fs from source isn't too bad at all!) I > also made your tweak to configure.in and then

Re: [Freesurfer] Any updates on recon-all GPU support?

Hi Richard, I resolved the make error. Just needed to point my libcudart.so in /usr/local/cuda/lib to the 64-bit equivalent in /usr/local/cuda/lib64. Running into other cuda-related issues with gcc now, but that should be much easier to resolve. -Derek

[Freesurfer] Qdec-correction for multiple comparison

Dear FS experts, I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison. In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend montecarlo or FDR. Are there

[Freesurfer] Research Specialist Job Opening at the Center for Healthy Minds

Research Specialist-86782 The Center for Healthy Minds (CHM), a component of the Waisman Center, was founded and is led by neuroscientist Richard J. Davidson. CIHM's mission is to cultivate well-being and relieve suffering through a scientific understanding of the mind. CHM is a leader in

Re: [Freesurfer] freeview display problem

May be thats the problem. I'll try to give it a shot to see if it fixes the problem. Thanks. From: Ramtilak Gattu Sent: Thursday, June 23, 2016 4:10:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: freeview display problem This issue is only with

Re: [Freesurfer] Any updates on recon-all GPU support?

Hi Richard, Hope this finds you well. I followed your instructions and compiled from source (you were right-- compiling Fs from source isn't too bad at all!) I also made your tweak to configure.in and then ran ./configure like so: ./configure --disable-Werror --enable-fermi-gpu

Re: [Freesurfer] qdec load error missing BLT

contents of $FREESURFER_HOME/lib/tcl/ allisons_surfaces.tcl offsetmovie.tcl TclChartWindow.tcl curv-flat.tcl phasemovie.tcl test_layers.tcl curv-views.tcl polar-flat.tcl test_ScubaFrame.tcl dara_data.tcl polar-views.tcl test_ScubaLayers.tcl

[Freesurfer] qdec load error missing BLT

When loading qdec I get can't find package BLT FsgdfPlot::InitFsgdf: Couldn't find fsgdfPlot.tcl on Ubuntu with FreeSurfer5.3 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] freeview display problem

So it happens with freeview all the time? Freeview uses openGL as backend for rendering, which I believe is not the case for fslview. Would it be possible for you to update your graphics card driver? > On Jun 23, 2016, at 4:10 PM, Ramtilak Gattu wrote: > > This issue is

Re: [Freesurfer] freeview display problem

This issue is only with freesurfer , images on fslview doesnt have this problem. From: Ramtilak Gattu Sent: Thursday, June 23, 2016 3:31:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: freeview display problem That is just one layer the yellow contrast

Re: [Freesurfer] freeview display problem

That’s indeed strange. I wonder if it is a graphics card issue. Does the blue tone appear all the time? on any volume? > On Jun 23, 2016, at 3:31 PM, Ramtilak Gattu wrote: > > That is just one layer the yellow contrast is from when we tune the contrast > up or down. >

Re: [Freesurfer] freeview display problem

That is just one layer the yellow contrast is from when we tune the contrast up or down. From: Ramtilak Gattu Sent: Thursday, June 23, 2016 2:37:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: freeview display problem Hello , I am having strange freeview

Re: [Freesurfer] freeview display problem

Is there any other layer loaded? It looks like there is at least another overlay on top of the volume layer? Best, Ruopeng > On Jun 23, 2016, at 2:37 PM, Ramtilak Gattu wrote: > > Hello , > > I am having strange freeview display problem. The images doesnt appear in >

Re: [Freesurfer] patch error

no problem. The stride error is something buried in the depths of openGL. It seems to be OS/version specific and there isn't much we can do about it Glad you figure out your error though Bruce On Thu, 23 Jun 2016, S.V.Shepherd [work] wrote: The error on flattening was caused by my saving

Re: [Freesurfer] patch error

Thanks for the update. This information could be of potential help if this error is ever come across again by other users. -Zeke On 06/23/2016 01:53 PM, S.V.Shepherd [work] wrote: > The error on flattening was caused by my saving the surface, instead of > the patch, to lh.full.patch.3d. I

Re: [Freesurfer] patch error

The error on flattening was caused by my saving the surface, instead of the patch, to lh.full.patch.3d. I apologize -- it was a dumb mistake. I am unsure what caused the """ Assertion `a[j].inputstride == vptr->stride' failed. """ error, but it only occurred on a few attempts, so I was able to

[Freesurfer] Qdec

Dear Freesurfer experts, I wanted to run cortical thickness analysis between two groups to check the diffetence in thickness between the groups. I used Qdec My question is regarding correcting for multiple comparisons. There are two options FDR and montecarlo. Which option do you recommend? Are

Re: [Freesurfer] patch error

hmmm, are you sure that the partition isn't full or something? On Thu, 23 Jun 2016, S.V.Shepherd [work] wrote: $ tksurfer ${subj} lh inflated -sulc 1) closed cut line around corpus callossum etc. 2) four tension relief cuts 3) select connected region 4) save as patch stephen v.

[Freesurfer] BrainSeg Volume Clarification

All, Upon looking at online forums and the FreeSurfer wiki, I have come to the understanding that "BrainSeg" volume in the aseg.stats file includes all cortical and subcortical gray matter, cerebellar gray matter; cortical, subcortical and cerebellar white matter and white matter

Re: [Freesurfer] recon-all warnings

Yes they are just warning and can be ignored. The upcoming release of freesurfer v6 has addressed the deprecation issue. -Zeke On 06/23/2016 11:48 AM, Rockers, Elijah D. wrote: > Hello, > > Doing a recon-all -all yields some deprecation warnings. > > defined(@array) is deprecated at >

Re: [Freesurfer] patch error

I should also note that I have had a couple problems, trying to fill the uncut area, where I get the following error: --- tksurfer.bin: ../../src/mesa/tnl/t_vertex.c:423: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. Abort (core dumped) --- *stephen v. shepherd phd*

[Freesurfer] recon-all warnings

Hello, Doing a recon-all -all yields some deprecation warnings. defined(@array) is deprecated at /freesurfer/mni/bin/nu_estimate_np_and_em line 165. Use of ?PATTERN? without explicit operator is deprecated at /freesurfer/mni/bin/sharpen_volume line 153. I think my results should still be OK

Re: [Freesurfer] doubts

Does that file exist? What is in it? If it is empty, it may bneed to be regenerated for that subject. Run recon-all -s subject -segstats On 6/22/16 7:17 PM, Elias Vergílio Da Cás wrote: Hi, *After the command: * asegstats2table --subjects AntonioMagnani -- meas volume --tablefile

Re: [Freesurfer] patch error

$ tksurfer ${subj} lh inflated -sulc 1) closed cut line around corpus callossum etc. 2) four tension relief cuts 3) select connected region 4) save as patch *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699 On Thu, Jun

Re: [Freesurfer] Converting fsaverage to MNI space

Try mri_vol2vol --targ fsaverage.DKT40+aseg.nii --mov /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz --o fsaverage_MNI_DKT40+aseg.nii --interp nearest --reg /Applications/freesurfer/average/mni152.register.dat --inv On 6/22/16 12:45 AM, Skyler Gabriel Shollenbarger wrote: Hi FS

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

You have no HDFemales so the 2nd column is 0. On 6/21/16 7:40 PM, Arkadiy Maksimovskiy wrote: Hello, Hello, I am getting the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Command line: mri_glmfit --y

Re: [Freesurfer] FSFAST- Cerebellum

After you run preproc-sess, there will be a file called register.dof6.dat. Map fmri into the anatomical space, something like mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o fmcpr.anat.nii.gz Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz However, I

Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28

I can see it so I don't know what the problem is. The script is short, so I've just copied it below. #!/usr/bin/python # This script replaces carriage returns with line feeds # Usage: rmcr inputfile > outputfile > # $Id: rmcr,v 1.1 2015/03/24 21:56:02 greve Exp $ import sys; import fileinput;

Re: [Freesurfer] Recon-all error at Talaraich transform

Hello, Usually this error only occurs when using the the mni tools with the perl (version 5.22 or higher). But Yosemite should be pre 5.22 so Im not sure why your encountering that issue. Can you upload me you subject data so I can take a look?

[Freesurfer] RA position available

The UCSF Department of Radiology and Biomedical Imaging is looking for a researcher with strong interests in neuroimaging interested in a Specialist position at UCSF. We are a neurodevelopment and neuroimaging lab. Specialists (research assistant) appointed at the junior rank must possess a

Re: [Freesurfer] patch error

Hi Stephen how did you create the patch? It looks like it is corrupted since that vertex # is way too big. The total # of vertices in the patch is also wrong. cheers Bruce On Thu, 23 Jun 2016, S.V.Shepherd [work] wrote: Hello all, I'm trying to make a patch and have run into the 'bad

Re: [Freesurfer] Any updates on recon-all GPU support?

Hi Richard, Thanks again for the quick response. I am able to compile CUDA programs from the SDK, so I will try to compile from the Fs source per the advice that you provided and see what happens. Will let you know how it goes! -Derek From:

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

Thanks very much Thomas. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

You should be able to use the 5.3 version. Regards, Thomas On Thu, Jun 23, 2016 at 2:16 PM, Bronwyn Overs wrote: > Hi Thomas, > > Thanks for your reply. > > The fsaverage directory I have for fs v 5.1 does not include the lh and rh > Yeo2011_7Networks_N1000.annot files. I

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

Hi Thomas, Thanks for your reply. The fsaverage directory I have for fs v 5.1 does not include the lh and rh Yeo2011_7Networks_N1000.annot files. I only have this in the 5.3 version of fsaverage. Can I still use the 5.3 version annot files or would I need a seperate set processed with