Freesurfer

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19 participants
30088 discussions

"CorticalWhiteMatterVol" ?
by Gonzalo Rojas Costa 11 Feb '19

11 Feb '19

External Email - Use Caution Hi: What is the meaning of the "CorticalWhiteMatterVol" measure? Sincerely, Gonzalo Rojas Costa

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PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output
by Matthieu Vanhoutte 11 Feb '19

11 Feb '19

External Email - Use Caution Dear Douglas, Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according your advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, final values at each voxel are not the same… To obtain first rescaled voxel-wise output I have used sequentially these steps: 1. Concatenate transforms from PET space to gtmseg.mgz 2. Register native PET into gtmseg space (trilin. interpolation) 3. Compute mean PET inside reference regions (with regions masks from gtmseg.mgz) 4. Compute intensity normalized PET images in gtmseg space Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command use these same steps ? Best, Matthieu

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hippocampus subfield division
by Yixin Ma 11 Feb '19

11 Feb '19

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask about the hippocampus subfield division again. Last time, I gave you an example of the subject that I failed to run the hippocampal subfield division, and you told me that you were able to run the hippocampus subfield on your laptop. I was using the older command of recon-all -all -s bert -hippocampal-subfields-T1. Should I try to use the newer version: segmentHA_T1.sh bert [SUBJECTS_DIR]. Is that possible FreeSurfer upgrading is the reason that I failed to run a subject on my server recently (but I was able to run it before). Also, can I ask where can I find the file of segmentHA_T1.sh? Thanks for your help. Cheers, Yixin

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Runtime of Freesurfer on Linux VM on Google Cloud Platform
by Yi-Fang Chuang 10 Feb '19

10 Feb '19

External Email - Use Caution Dear Freesurfer developers and users, Has anyone had experience running Freesurfer on Linux VM on Google Cloud Platform? I have a question about runtime of recon-all -all. The specs of VM on GCP as follows, Linux CentOS 6, 16 CPU(Intel(R) Xeon(R) @ 2.50GHz) with 60 G memory I installed Freesurfer v 6.0.0 and run recon-all -all -parallel -openmp num No matter what number I put (6,8,12,16 after openmp), the recon-all runtime of a single subject ranges 6-7 hours. It's just disappointing to compare to my own desktop. My own Desktop is Mac Pro (3.7 GHz quad-core intel xeon E5, 16G memory). The recon-all runtime (Freesurfer version 5.3.0, no parallel) for a single subject is usually 7~8 hours. Is this a reasonable runtime given the setting of VM? Only 1-2 hour shorter than my Mac Pro?? Or is there any configuration of VM I should pay attention to set up? Thanks, Yi-Fang Chuang ᐧ ᐧ

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issues with bvecs extracted from dicoms
by Vincent.Beliveau＠i-med.ac.at 09 Feb '19

09 Feb '19

External Email - Use Caution Dear FreeSurfer team! First of all, thanks for the great tools! I have recently started to work with DWI data and there are a few issues I was hoping you could help me with. I have recently found a post on the FSL mailing list mentioning that the bvecs stored in the dicoms header on Siemens scanner are corrected for slice angulation (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;5757c231.1005) I assume this means that, for Siemens dicoms, the bvecs are stored in image orientation? Indeed, the bvecs in the dicoms are different than the ones in the table provided by Siemens. When looking at the preprocessing performed by tracula, the flag --bvec-voxel is used when importing the data from dicoms; isn't this be conflicting with the fact that the bvecs are already in image orientation? A second issue I have is when using the bvecs extracted using tracula to perform tractography in trackvis/diffusion toolkit. For some stange reason, I have to flip the z-axis of the bvec (obtained with either --bvec-voxel or --bvec-scanner) to obtain sensible tractography results. When comparing the bvecs from tracula to the table from Siemens the z-axis is indeed flipped. Unfortunately, this flip issue also occurs in a number of other conversion software (e.g. dcm2niix, mrtrix). Does anyone know where this could be coming from? Note, my data was acquired on a Siemens SkyraFit with software version VE11C. Finally, does anyone know what orientation (image/scanner) is expected for the bvecs when using dti_tracker (in diffusion toolkit)? When looking at the default bvec file passed through the GUI interface to dti_tracker, it seems that it requires bvecs in scanner orientation, but I would like to confirm this. Unfortunately, I did not receive any reply to my emails to support(a)trackvis.org. Perhaps someone on this list knows? Thanks in advance! Vincent.

1 0

Find the fsaverage voxel that corresponds to a voxel in the raw Nifti file
by ts+ml＠rcmd.org 09 Feb '19

09 Feb '19

External Email - Use Caution Dear FreeSurfer experts, I have a raw nifti file created from a stack of DICOM scanner images, let's say it has dimension (162, 172, 188) along the 3 axes. I have also pre-processed this subject in FreeSurfer and have the resulting volume files (e.g., orig.mgz) available. My question is: For a given voxel in the raw nifti file, how could I find the voxel (or coordinate) in the fsaverage subject that corresponds to this voxel? I guess this should be a 2 step process: - first get and apply the affine matrix that leads from the raw file to the Freesurfer pre-processed version (which is resampled to dimension (256, 256, 256) among other changes) - then get and apply the matrix that leads from the pre-processed subject to fsaverage But where exactly can I get these matrices from? I guess the talairach.xfm file and some volume like orig.mgz (using mri_info)? Best, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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ExploreDTI Workshop in May@Budapest
by Szabolcs David 08 Feb '19

08 Feb '19

External Email - Use Caution ExploreDTI Workshop - A course on processing, analyzing, and visualizing diffusion MRI data When: 27-29 May, 2019 Where: Budapest, Hungary Details: http://www.exploredti.com/workshop Cheers, Szabolcs >

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[PETSurfer] Intensity normalization of PET images without PVE correction
by Matthieu Vanhoutte 08 Feb '19

08 Feb '19

External Email - Use Caution Dear Douglas, Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ? Best, Matthieu

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Re: [Freesurfer] Trouble Installing FreeSurfer {Disarmed}
by fsbuild 07 Feb '19

07 Feb '19

External Email - Use Caution Hello Rodrigo, You could also try installing freesurfer into you home directory and make sure that works - before trying to install into /usr/local. I am attaching a file that lists and explains the commands I used to install freesurfer into my home directory on an Ubuntu 16..04 machine. You should be able to cut and paste the commands with the exception of perhaps the location of the freesurfer 6.0.0 release archive and the license.txt file, which I put into my downloads directory ($HOME/downloads). - R. On Feb 1, 2019, at 18:04, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Rodrigo,Please use capital -C and not lowercase -c to tell the tar command what directory to untar the files into; you used -C the first time when the file could not be found, but on the subsequent commands you changed it to -c - R.tar -C /eeg/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gzRodrigo Montenegro  at 13:42 2/01/2019        External Email - Use Caution        Hey! I have not received any feedback from that… Not sure if the mail was lost?...  Any help would be appreciated! Kind Regards, Rodrigo Montenegro+44(0)7503070807 From: Rodrigo Montenegro [mailto:rmontenegro11@gmail.com] Sent: 30 January 2019 20:39To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>Cc: 'rodrigo.montenegro(a)ndcn.ox.ac.uk' <rodrigo.montenegro@ndcn.ox.ac.uk>Subject: RE: [Freesurfer] Trouble Installing FreeSurfer {Disarmed}Importance: High Hi R, Thanks for the quick response. I have but still couldn’t go through the process. I have also read your e-mail but I have no idea what you refer to in your second e-mail. This is what I have got:  Kind Regards, Rodrigo Montenegro+44(0)7503070807 From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh..harvard.edu] On Behalf Of fsbuildSent: 28 January 2019 23:17To: freesurfer@nmr.mgh.harvard..eduCc: rodrigo.montenegro@ndcn.ox.ac.ukSubject: Re: [Freesurfer] Trouble Installing FreeSurfer {Disarmed}         External Email - Use Caution        … Correction - with the v switch “tar -xzvf” it is going to list every fileit expands and then return to the “$” prompt. - R._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Vertex-wise area anlaysis
by Klaas Bahnsen 07 Feb '19

07 Feb '19

External Email - Use Caution Dear Freesurfer Experts, First of all: Thank you so much for your work and your fantastic product. I turn to you with a short question, I hope it is not too unnecessary and can be answered quickly. My interest lies in vertex wise longitudinal investigation of cortex surface area. The paper 'False positive rates in surface-based anatomical analysis' (Greve, Fischl 2018) briefly describes how Freesurfer calculates cortex surface areas: First the transfer to the target atlas with "Jacobian Correction" and second the division by eTIV (ICV) to include the factor of different head sizes. Finally, a smoothing should be applied. My question is where these data are stored in the Freesurfer data structure or where they are generated. My understanding is that first recon-all stores this data per scan under SubjectID/surf/?h.area. These could then be picked up by mris_preproc and smoothed with mri_surf2surf. This smoothed file could then be used for example for a GLM model (mri_glmfit). Are the steps described in the paper covered with this workflow? Or must a special option be selected at some point, e.g. to perform the division by the eTIV. I'm a bit unsure at the moment because I also found a collection of questions from previous courses on the FreeSurfer Wiki page. In course 2014 Copenhagen the question is asked which units are used in the output files which are calculated by mris_preproc. Part of the answer states that the data in ?h.area.mgh on vertex level do not have much meaning, because they are dependent on the triangle mesh. Hopefully you can help me and hopefully I won't steal you too much time with my question. With kind regards, Klaas Bahnsen

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