Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

External Email - Use Caution Hi Douglas, Could you help me concerning my previous questions ? Thanks, Matthieu > Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE a > écrit : > > Hi Douglas, > > Thanks for clarification. Why use "nearest neighbor" instead of classical > "triline

Re: [Freesurfer] problem using recon-all

External Email - Use Caution Hey, So I disabled SIP, and tried to run the subject from the beginning, and sadly I encountered an error while running the PreFreesurfer Pipeline, which worked fine until disabling SIP. This is the error message: ** ERROR (nifti_image_read): short

Re: [Freesurfer] problem using recon-all

External Email - Use Caution you can ignore the nifti errors in the beginning of the error message, because it was just a small glitch that I solved. the rest of the errors still stand, and are unclear to me.. On Thu, 14 Feb 2019 at 11:09, Shachar Gal wrote: > Hey, > So I disabl

[Freesurfer] Submission deadline for #BrainTC extended

External Email - Use Caution Dear colleagues, the deadline for submitting abstracts to the 3rd annual Brain Twitter Conference has been extended - the new deadline is 20th February. The line-up of keynotes is now: prof. Jay van Bavel, New York University (social neuroscience) p

Re: [Freesurfer] Task Design Question

Hello Freesurfer experts, I am working on designing a task using opt seq to determine the optimal ITI and I had a question about task timing. Does it matter if the stimulus period during a task starts at the start of a TR or that the stimulus presentation lasts uninterrupted an amount of tim

[Freesurfer] -so unknown in mri_surf2vol?

External Email - Use Caution My_pc$ mri_surf2vol --o 0021_thickness-in-volume.nii.gz --subject 0021 \ --so $SUBJECTS_DIR/0021/surf/lh.white $SUBJECTS_DIR/0021/surf/lh.thickness \ --so $SUBJECTS_DIR/0021/surf/rh.white $SUBJECTS_DIR/0021/surf/rh.thickness ERROR: Option --so unkno

[Freesurfer] Unexpected termination of freeviewer

External Email - Use Caution Hi, I used freeviewer a few weeks ago without any problems, but now that I want to continue my analysis it terminates as a try to load a volume or a surface. (same computer, same setting) I have tried the “sudo -E fs_update” and to disable SIP, freevi

Re: [Freesurfer] -so unknown in mri_surf2vol?

Remove the backslashes On 2/14/19 10:15 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > My_pc$ mri_surf2vol --o 0021_thickness-in-volume.nii.gz --subject 0021 > \ --so $SUBJECTS_DIR/0021/surf/lh.white > $SUBJECTS_DIR/0021/surf/lh.thickness \ --so > $SUBJECTS_DIR/0021/sur

Re: [Freesurfer] License Registration Error "Spammer, go away!"

External Email - Use Caution Then it was the Firefox's built-in auto-fill triggered the spam detection. Finally got the license file. Thanks. On Wed, Feb 13, 2019 at 4:18 PM Hoopes, Andrew wrote: > Are you using some sort of form auto-fill plugin when you're accessing the > reg

Re: [Freesurfer] Task Design Question

Are you going to do an FIR analysis or are you going to assume a shape to the hemodynamic response function? If you are assuming the shape (the usual), then the answer to both of your questions is no On 2/14/19 8:31 AM, Rockhill, Alexander P. wrote: > Hello Freesurfer experts, > >    I am workin

Re: [Freesurfer] Sections of Temporal Lobe not included

hard to tell from those images what is happening. Can you send an image with an arrow pointing to where the problem is? Putting the brain right-side-up will be helpful as well On 2/14/19 8:12 AM, John Mc Fadden wrote: > > External Email - Use Caution > > Hi, > > I have processed two subj

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

The GTM operates on regions, so you can't do trilin interp. The operations that you describe below are not used in mri_gtmpvc. If  you are trying to get something close to what the GTM does, then use nearest neighbor On 2/14/19 3:43 AM, Matthieu Vanhoutte wrote: > External Email - Use

Re: [Freesurfer] dt_recon issue

what happens when you run ls -l /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm On 2/13/19 6:45 PM, Daniel Callow wrote: > > External Email - Use Caution > > Here it is. > > > [hlhp-105:DANIEL/scripts/dti_freesurfer] administrator% dt_recon > --debug --i > /Volumes/DA

Re: [Freesurfer] GLM - correction for multiple comparisons

It is certainly possible. Are some of the clusters in abs negative? Also, I would strongly recommend using permutation if you are using such a low clusterwise threshold. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm The monte carlo simulation is not valid a

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

External Email - Use Caution Hi Douglas, So to register PET to gtmseg space mri_gtmpvc command use nearest neighbor, interpolation right ? And what about the interpolation method to use when projecting PVE corrected PET on surface  ? Thanks, Matthieu On 14/02/2019 17:44, Gre

Re: [Freesurfer] GLM - correction for multiple comparisons

There are no negative clusters in abs. I tried to apply the permutation but it says it requires an orthogonal matrix. Right now I am using this: -1 1 0 0 How would my orthogonal matrix look like? Thanks, Vale From: freesurfer-boun...@nmr.mgh.harvard.edu on

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote: > External Email - Use Caution > > Hi Douglas, > > So to register PET to gtmseg space mri_gtmpvc command use nearest > neighbor, interpolation right ? It does not map the PET to the gtmseg space. It maps the gtmseg to the PET space. Since t

[Freesurfer] Pediatric Cortical Thickness Normalization by ICV

External Email - Use Caution Hi, I am running an analysis in a group of pediatric subjects (4-6 years old) and want to correct cortical thickness values by ICV before running the statistical model, since we have limited degrees of freedom. While I know this is not recommended f

[Freesurfer] fsgd and contrasts

External Email - Use Caution Hi, I realize this is fairly straightforward for most of you, but I am relatively new to freesurfer and want to make sure I'm proceeding correctly with group analysis. We have ~35 TBI subjects and a similar number of age- and sex-matched controls, a

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

External Email - Use Caution Le jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> a écrit : > > > On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote: > > External Email - Use Caution > > > > Hi Douglas, > > > > So to register PET to gtmseg space mri

Re: [Freesurfer] Pediatric Cortical Thickness Normalization by ICV

External Email - Use Caution Got it, that exactly what I was looking for! Thank you very much. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, February 14

Re: [Freesurfer] talairach.m3z question

Hi oTim sorry, it's not well documented, but the I/O code is distributed if you want to take a look. The .m3z stores a dense deformation field, plus some associated information such as the input and output ras2vox matrices, the resolution of the mesh, etc... cheers Bruce On Wed, 13 Feb 2019,

Re: [Freesurfer] Unexpected termination of freeviewer

Hi, you were able to use freeview before without it crashing – have you made any changes to the distribution since then? Are you sure that you’ve set FREESURFER_HOME and sourced the FS environment before calling freeview? Andrew From: on behalf of Lykke Silfwerbrand Reply-To: FS Help Date:

Re: [Freesurfer] Pediatric Cortical Thickness Normalization by ICV

There is not something that will plug-and-play for this. But you can do something like cd subject/surf fscalc lh.thickness div ETIV -o lh.thickness.etiv.mgz where ETIV is from the aseg.stats file Then specify --meas thickness.etiv.mgz when running mris_preproc On 2/14/19 12:50 PM, Williamson, B

Re: [Freesurfer] Pediatric Cortical Thickness Normalization by ICV

btw, I just added this feature to mris_preproc, so, in the next version you will only need to add --etiv to the command line. On 2/14/19 1:17 PM, Williamson, Brady wrote: > External Email - Use Caution > > Got it, that exactly what I was looking for! Thank you very much. > > -Origina

Re: [Freesurfer] Pediatric Cortical Thickness Normalization by ICV

External Email - Use Caution Fantastic! I look forward to the next release. Thank you again for your responsiveness. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sen

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > > > > Le jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> a écrit : > > > > On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote: > >          External Email - Use Cauti

Re: [Freesurfer] fsgd and contrasts

On 2/14/19 1:04 PM, John Absher wrote: > > External Email - Use Caution > > Hi, I realize this is fairly straightforward for most of you, but I am > relatively new to freesurfer and want to make sure I’m proceeding > correctly with group analysis. > > We have ~35 TBI subjects and a sim

Re: [Freesurfer] Missing files after recon-all

did you try looking in the output to see if those files are actually there? On 2/13/19 1:11 PM, Zhi Li wrote: > > External Email - Use Caution > > Hello FreeSurfer experts, > > I am trying recon-all in a SGE cluster. However, the size of of the > results was smaller than that executed in

Re: [Freesurfer] Unexpected termination of freeviewer

External Email - Use Caution Hi, Yes, I am sure that I set the FREESURFER_HOME and sourced SetUpSurfer.sh I haven’t made any changes. Also, I can open the freeview GUI, it only crashes when I try to load something. I have no problem running recon all on the two machines either (t

Re: [Freesurfer] problem using recon-all

Is python being called from matlab here? It probably has to do with how matlab sets DYLD_LIBRARY_PATH. I would maybe try using pip to uninstall and reinstall the fslpython scipy package, but that might be dangerous - I’m not sure how fsl sets up its python env. I’ll look into it a bit more and g

Re: [Freesurfer] Unexpected termination of freeviewer

How are you opening the freeview GUI? Andrew From: on behalf of Lykke Silfwerbrand Reply-To: FS Help Date: Thursday, February 14, 2019 at 1:47 PM To: FS Help Subject: Re: [Freesurfer] Unexpected termination of freeviewer External Email - Use Caution Hi, Yes, I am sure that I set the

[Freesurfer] surface cortical lesions mask --> annotation file ???

Dear Freesurfers, I need to extract annotation files from my cortical lesion masks projected to the surface. Do you know whether this is possible? Thank you, Valeria ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harv

[Freesurfer] Thalamic nuclei segmentation

External Email - Use Caution Hi! Few weeks ago I found the thalamic nuclei segmentation tool in Freesurfer development version and I had it working fine. However, I can’t find the web page anymore with the instructions how to use the tool. Is the tool still in use and if so, wh

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

External Email - Use Caution > Le 14 févr. 2019 à 19:37, Greve, Douglas N.,Ph.D. a > écrit : > > > > On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote: >> >> External Email - Use Caution >> >> >> >> Le jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D. >> mailto:dgr..

Re: [Freesurfer] Missing files after recon-all

External Email - Use Caution Yes I checked but these files are not there. I only found 'talairach.m3z' under '/mri/transforms' and some label files end with 'exvivo.label' under '/label', such as 'lh.BA1_exvivo.label' and 'lh.BA1_exvivo.thresh.label'. Thanks and best wishes, Lizh

Re: [Freesurfer] Missing files after recon-all

can you send the recon-all.log file? On 2/14/19 2:55 PM, Zhi Li wrote: > > External Email - Use Caution > > Yes I checked but these files are not there. I only found > 'talairach.m3z' under '/mri/transforms' and some label files end with > 'exvivo.label' under '/label', such as 'lh.BA1_e

Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

not sure what you mean, can you elaborate? On 2/14/19 2:05 PM, Barletta, Valeria wrote: > > Dear Freesurfers, > > I need to extract annotation files from my cortical lesion masks > projected to the surface. > > Do you know whether this is possible? > > Thank you, > > Valeria > > > ___

Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

Yes sure, I need to extract values from discrete cortical lesions, but I have masks of all lesions together projected to the cortical surface. I have a script that can provide me values for every single lesion separately, but this script works on annotation files. Is it possible to create an an

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

On 2/14/19 2:25 PM, Matthieu Vanhoutte wrote: > External Email - Use Caution > >> Le 14 févr. 2019 à 19:37, Greve, Douglas N.,Ph.D. a >> écrit : >> >> >> >> On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote: >>> External Email - Use Caution >>> >>> >>> >>> Le jeu. 14 févr. 2019 à 1

Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

You can make separate labels (mri_cor2label with --surf option), then use mris_label2annot On 2/14/19 3:32 PM, Barletta, Valeria wrote: > > Yes sure, > I need to extract values from discrete cortical lesions, but I have > masks of all lesions together projected to the cortical surface. > > I hav

Re: [Freesurfer] dt_recon issue

External Email - Use Caution Hi Douglas, I was unsure if the emails I had been replying with were going through. They did not seem to come up on the mailing list so I wasn’t sure if they had reached you. I recently responded to your question about the ls -l path output and the —de

Re: [Freesurfer] dt_recon issue

I never saw an email with the result of the ls -l command On 2/14/19 3:36 PM, Daniel Callow wrote: > > External Email - Use Caution > > Hi Douglas, > > I was unsure if the emails I had been replying with were going > through. They did not seem to come up on the mailing list so I wasn’t >

Re: [Freesurfer] Thalamic nuclei segmentation

http://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei On 2/14/19 2:21 PM, Antti Cajanus wrote: > External Email - Use Caution > > Hi! > > Few weeks ago I found the thalamic nuclei segmentation tool in Freesurfer > development version and I had it working fine. However, I can’t find th

Re: [Freesurfer] Unexpected termination of freeviewer

External Email - Use Caution Clicking the icon in the freesurfer library. Lykke 14 feb. 2019 kl. 19:50 skrev Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>>: How are you opening the freeview GUI? Andrew From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Lykke

Re: [Freesurfer] Missing files after recon-all

The log file indicates that everything finished successfully. The m3z.inv files are no longer created. The label files are now called, eg, lh.MT_exvivo.label (they have "exvivo" in them). I don't know why the checker is not working, probably needs to be updated for version 6. I don't think a lo

Re: [Freesurfer] Unexpected termination of freeviewer

You need to load freeview from the terminal. FREESURFER_HOME is not set and freesurfer is not sourced when you load freeview from an icon – however, this is supported in the dev release. Source freesurfer and run `freeview` on the command line. best Andrew From: on behalf of Lykke Silfwerbran

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution Hi Doug, Could you advise me about how to correctly run mri_vol2vol? The functional data did not get perfectly registered to the anatomy so I'm afraid I'm not running it correctly. Thanks! Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl < fis.

Re: [Freesurfer] dt_recon issue

you can only give it one dicom file from the series, it will find the rest. On 2/14/19 4:11 PM, Daniel Callow wrote: > > External Email - Use Caution > > As you can see the folder has 65 DICOM images labeled > images01.dcm-images65.dcm. > > I tried > > dt_recon --i > /Volumes/DAN

Re: [Freesurfer] registration and resampling in native space

Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2 weighted? If so, you should use --t2 instead of --t1 in bbregister On 2/14/19 2:18 PM, Francesca Strappini wrote: > > External Email - Use Caution > > Hi Doug, > > Could you advise me about how to correctly run mri_vol2vol? > The fun

Re: [Freesurfer] Missing files after recon-all

External Email - Use Caution I see. Thank you very much. Best wishes, Lizhi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

External Email - Use Caution Le jeu. 14 févr. 2019 à 21:36, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> a écrit : > > > On 2/14/19 2:25 PM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > > > >> Le 14 févr. 2019 à 19:37, Greve, Douglas N.,Ph.D. < > dgr.

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

>>But in the case where --psf 0 --no-tfe are specified, isn't the high resolution of gtmseg lost when rescaling intensities to mean reference region ? Yes On 2/14/19 5:25 PM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > > > > Le jeu. 14 févr. 2019 à 21:36, Greve, Dougla

[Freesurfer] mris_preproc error: dimension mismatch

External Email - Use Caution Hi Everyone, I'm trying to prepare my Cerebral blood flow surface data for mri_glmfit group analysis (qdec doesn't allow you to choose your own subject surface files to analyze, so I figured mri_glmfit is my only option). Quick summary of what I did