Re: [Freesurfer] reading ?h.smoothwm.nofix

Can you email me the file? > On Apr 29, 2014, at 10:27 PM, Virendra Mishra > wrote: > > Hi Bruce, > > I tried read_surf. There is a line in read_surf.m "magic = > freesurfer_fread3("name of the surface_file")" The number returned into magic > does not match any of the predefined numbers for

Re: [Freesurfer] reading ?h.smoothwm.nofix

Hi Bruce, I tried read_surf. There is a line in read_surf.m "magic = freesurfer_fread3("name of the surface_file")" The number returned into magic does not match any of the predefined numbers for quad or tri type of file and hence it throws an error for vertices because vertices get assigned in

Re: [Freesurfer] reading ?h.smoothwm.nofix

Hi Virendra Is that our function? I haven't heard of it. Have you tris read_surf? Bruce > On Apr 29, 2014, at 4:16 PM, Virendra Mishra > wrote: > > Hello Bruce, > > Thank you for the quick reply. Essentially, I want to use > find_corresponding_center_FSformat matlab command with ?h.smoothwm.n

Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3

No, once you've got the orientation correct, then it should be fine On 04/29/2014 08:03 PM, prasser wrote: > Other than orientation, (which could be deduced from visual inspection > of fiducial markers or other) are there any other concerns with this > approach? > Paul > > > On Tue, 29 Apr 2

Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3

Other than orientation, (which could be deduced from visual inspection of fiducial markers or other) are there any other concerns with this approach?Paul On Tue, 29 Apr 2014 09:04:00 -0700 Douglas N Greve wrote I don't know that it would be preferred o

Re: [Freesurfer] p values for within-subject t maps

Thank you, much appreciated! > > Is this the same question posted yesterday on martinos-tech? I answered > it as below > > Yes, those are in the sig.nii.gz file (these are -log10(p)). The DOF is > related to the number of TRs > doug > > On 04/29/2014 04:49 PM, jaco...@nmr.mgh.harvard.edu wrote: >>

[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Thank you very much Michael. Now I'm running probtrackx, I will update you. Stefano Messaggio originale Da: mha...@wustl.edu Data: 29-apr-2014 22.25 A: "std...@virgilio.it", "freesurfer@nmr.mgh.harvard.edu", "Harms, Michael" Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R

Re: [Freesurfer] p values for within-subject t maps

Is this the same question posted yesterday on martinos-tech? I answered it as below Yes, those are in the sig.nii.gz file (these are -log10(p)). The DOF is related to the number of TRs doug On 04/29/2014 04:49 PM, jaco...@nmr.mgh.harvard.edu wrote: > -- Forwarded message -- > H

Re: [Freesurfer] Coordinate transformation to average surface space

The purpose of what I'm trying to do is getting specific points from the CT onto the average surface. These points lie on the surface of the brain. Originally, we were using flirt to register the CT to the MRI, then registering the MRI to the talairach brain, to get the CT into the same space as t

[Freesurfer] p values for within-subject t maps

-- Forwarded message -- Hello Doug et al., I was wondering if anyone could give me some information about whether a p value can be associated with t maps generated in individual subjects (across one or two runs) for fMRI data. When doing group contrasts an uncorrected p value can b

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Yes, the S/I/A/P labels are all correct.  (Can never tell with R/L). So, FSLview is reading the orientation info correctly.  Orientation, as coded in the NIFTI, is a completely separate issue from how a given viewing tool chooses to display the data.  You may not like the manner in which FSL

Re: [Freesurfer] reading ?h.smoothwm.nofix

Hi again! I tried read_surf() with ?h.smoothwm.nofix surface file and it throws an error..essentially still to do with magic number. Any help is greatly appreciated. Thank you. Sincerely, Virendra. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-bo

Re: [Freesurfer] reading ?h.smoothwm.nofix

Hello Bruce, Thank you for the quick reply. Essentially, I want to use find_corresponding_center_FSformat matlab command with ?h.smoothwm.nofix surface file which I believe calls freesurfer_fread3() file and throws an error "Unknown magic number in surface file ?h.smoothwm.nofix. How do I get t

Re: [Freesurfer] reading ?h.smoothwm.nofix

Hi Virendra I think you can use read_surf.m for any of the binary (not named *.asc) surfaces. cheers Bruce On Tue, 29 Apr 2014, Virendra Mishra wrote: Hello all,   Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really

[Freesurfer] reading ?h.smoothwm.nofix

Hello all, Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices a

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Yes, they need to be the same dimensions to overlay in FSLview. Run 'mri_convert' on orig.mgz, and you should be able to underlay the orig. --  Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Wash

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

--  Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha.

[Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

I'm trying to do it. But I have an error. It shoud be due to difference in size? In freeviewer the files are shown in fslview no. fslinfo T1_STRUCT.nii.gz (T1 used for recon-all)data_type FLOAT32dim1 212dim2 320dim3 320dim4 1datatype 16pixdim1

Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL

You need to overlay the thalamus ROI on the T1 from which it was derived, so that I have a reference for the anatomy. It is very unlikely that FSLview is ignoring the orientation information. cheers, -MH --  Michael Harms, Ph.D.

Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Is the brain merely shown "sideways" in FSLview?  What matters is that the A/P/S/I/L/R labels are correct in FSLview, in which case the orientation info is read just fine, and it is solely a matter of how FSLview choses to display data that doesn't have an RAS/LAS orientation. cheers, -MH

Re: [Freesurfer] Segmentatoin fault using Freesurfer Functions Fedora 19 - Freesurfer 5.1

John, I just noticed that you are looking for v5.1, and that we don't have a centos6 build of that (we started those with v5.2). Can you try v5.3? N. On Tue, 2014-04-29 at 12:20 +, West, John D. wrote: > Hey Nick. > > Good idea. Is there a Centos6 version of Freesurfer 5.1 I can download

[Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Hi Bruce, in tkmedit the orientation is ok. Is wrong in fslview. Now, I'm running probtrackx. I'll update you on results. Thanks, Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 29-apr-2014 17.52 A: Ogg: Re: [Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL

Re: [Freesurfer] Coordinate transformation to average surface space

It sounds like you are doing the right thing with the right equation. Can you elaborate on what is going wrong? On 04/28/2014 05:10 PM, ISAAC PEDISICH wrote: > Sorry - I meant just the matrix. > > I'm trying to map from CRS in the CT to tkrRAS in the anatomical, I > believe. I'm a little uncle

Re: [Freesurfer] Problem with Monte Carlo Simulation

Upgrade! You can run the glm analysis in a new version and keep the old version for your individual analysis doug On 04/29/2014 01:06 PM, Jacqueline Elaine Fitzgerald wrote: > I'm using version 4.5.0. The --cache does not come up when I type the > command mri_glmfit-sim --help? > > Best, > > Ja

Re: [Freesurfer] Problem with Monte Carlo Simulation

I'm using version 4.5.0. The --cache does not come up when I type the command mri_glmfit-sim --help? Best, Jackie On 29 April 2014 16:58, Douglas N Greve wrote: > > what version are you using? There is also help when you run > mri_glmfit-sim --help > > On 04/29/2014 08:10 AM, Jacqueline Elain

Re: [Freesurfer] R: R: R: Filipping issue

You can't use qdec for this, you will have to use mris_preproc, mri_surf2surf, mri_glmfit, and mri_glmfit-sim. The first step is the tricky one in that you will have to run mris_preproc twice then merge the two data sets. For the subjects that you want the left hemisphere, run mris_preproc as

Re: [Freesurfer] A newbie to fMRI analysis

Have you tried using dcmunpack? You run it twice, once without any output to get a list of runs in the folder. The 2nd with how you want the data converted. Run it with --help to get more info doug On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: > Hello I have only recently started the fmri dat

Re: [Freesurfer] Xhemi: vertex-wise volume asymmetry analysis?

OK, you're using an older version that did not copy the volume. You can just do this cp subject/surf/lh.volume subject/surf/rh.volume Note the change from lh to rh! doug On 04/28/2014 06:25 PM, Yizhou Ma wrote: > Thanks Doug. I don't see an error message in xhemireg.?h.log files. > Please s

[Freesurfer] R: R: R: Filipping issue

Dear Doug, I registered with surfreg the hemispheres I would like to analyze. How should I proceed now for the final statistical vertex-wise analysis? Should I smooth the surfaces and perform between-group comparison with qdec? Thank you in advance Paola Paola Valsasina, MSc Research Fellow Neur

Re: [Freesurfer] FSL registration

If you have an example func of some kind, you can just run bbregister passing the example func with --mov. This will give you a register.dat file which can be used in mri_label2vol to map the subcortical seg into the function space. doug On 04/28/2014 06:18 PM, Jones, Richard wrote: > I have T

Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3

I don't know that it would be preferred or acceptable. You have just thrown away information about what is left and right, so you might have inadvertently flipped the brain. Unless your voxel size is 1mm, there will be some interpolation when conforming. I'm not that worried about the interpol

Re: [Freesurfer] incongruent coordinates in freeview and *sig.cluster.summary

The coords in the summary file are for the white surface, not the inflated. Try freeview again using the white surface On 04/29/2014 07:50 AM, Rujing Zha wrote: > Hi doug, > Thanks doug. > I saw the sig.mgh in freeview by typing this: > freeview -f > $SUBJECTS_DIR/fsaverage/surf/rh.inflated:ann

Re: [Freesurfer] Problem with Monte Carlo Simulation

what version are you using? There is also help when you run mri_glmfit-sim --help On 04/29/2014 08:10 AM, Jacqueline Elaine Fitzgerald wrote: > Hi Doug, > > I had not realised that was possible, thanks for that. Will save alot > of time! I am getting an error that the --cache flag is not > rec

Re: [Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL

How do you know the orientation is wrong? Is it right in tkmedit? On 04/29/2014 10:23 AM, std...@virgilio.it wrote: > My apologies, how can I visualize mri_binarize output? I tried in > fslview but orientation is wrong. Different orientation is a file's > feature or swapdim is request? > > Than

[Freesurfer] Two Research Assistant Positions at Boston Children's Hospital

Research Assistant Positions at Boston Children's Hospital: Pediatric and Infant (f)MRI/developmental cognitive neuroscience/typical and atypical reading development GaabLab at Children's Hospital Boston Developmental Medicine Children's Hospital Boston RESEARCH STUDY ASSISTANTS: Children's H

Re: [Freesurfer] A newbie to fMRI analysis

You could also try the nipy version. works real well with Snow Leopard OS shantanu On Mon, April 28, 2014 9:09 pm, Shantanu Ghosh wrote: > Hi Sampada, > > Please cc the freesurfer list when answering/asking questions so others > can answer too. And also people with similar issues will benefit fro

[Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL

My apologies, how can I visualize mri_binarize output. I tried in fslview but orientation is wrong. Different orientation is a file's feature or swapdim is request? Thanks, Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 29-apr-2014 16.01 A: , "Freesurfer support li

[Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL

My apologies, how can I visualize mri_binarize output? I tried in fslview but orientation is wrong. Different orientation is a file's feature or swapdim is request? Thanks, Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 29-apr-2014 16.01 A: , "Freesurfer support lis

Re: [Freesurfer] thalami mask (nii.gz) to import in FSL

Hi Stefano you can use either mri_binarize --match or mri_extract_label with labels 10 and 49 (which I got from FreeSurferColorLUT.txt) cheers Bruce On Tue, 29 Apr 2014, std...@virgilio.it wrote: Hi list, I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it as seed mask in

[Freesurfer] thalami mask (nii.gz) to import in FSL

Hi list, I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it as seed mask in probtrackx. Thanks, Stefano___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The in

[Freesurfer] Rendering in 3ds Max?

Hi list, Anybody has ever tried to bring Freesurfer pial surfaces for render in 3D studio max? I would be curious on the procedure to follow, more specifically on which file to export/import/convert. Thank you. Dorian TJU ___ Freesurfer mailing list Fr

Re: [Freesurfer] Segmentatoin fault using Freesurfer Functions Fedora 19 - Freesurfer 5.1

Hey Nick. Good idea. Is there a Centos6 version of Freesurfer 5.1 I can download somewhere? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky, MGH Sent: Monday, April 28, 2014 1:35 PM To: Freesurf

Re: [Freesurfer] Problem with Monte Carlo Simulation

Hi Doug, I had not realised that was possible, thanks for that. Will save alot of time! I am getting an error that the --cache flag is not recognised. This is the command I am running; [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_thickness_15 --cache 2.3 neg --cwp 0.05 ERROR: Flag --cac