Freesurfer

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30084 discussions

Re: [Freesurfer] T2 or FLAIR data to improve pial surfaces
by Glasser, Matthew 20 Jul '20

20 Jul '20

External Email - Use Caution What is the resolution of these images? Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Batra, Vinita R." <vbatra(a)lsuhsc.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, July 20, 2020 at 11:13 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] T2 or FLAIR data to improve pial surfaces External Email - Use Caution Dear FreeSurfer experts, I have both T2 and FLAIR images for the majority of the subjects in my study, and I want to use them to improve pial surface reconstruction during recon-all as explained in [1]. My questions are: 1) In general, should I prefer FLAIR over T2, or the other way around? 2) Some subjects (< 10%) do not have a FLAIR image, and others do not have a T2. Do you think that it is fine to use FLAIR for some subjects, and T2 for others, in the same study? We will perform manual QC after the recon-all run and exclude bad quality images so I wanted to hear your opinion. Best, VB ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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PetSurfer Crashing
by Crawford, Anna 20 Jul '20

20 Jul '20

External Email - Use Caution Hello, I am trying to run the PetSurfer process for the first time. I was able to run gtmseg and mri_coreg which seemed to go okay. When I tried running mri_gtmpvc, it is crashing, but I am not sure why. The command I am using and output are below. Do you have any guidance as to what is going wrong? Thank you, Anna mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o subject/gtmpvc.output Loading input ../CTPET/PET.template.nii.gz done loading input 1 frames $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /mnt/netRAID18/7T/study709/S2sdt/ cd /mnt/autofs/netRAID18/7T/study709/S2sdt mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o subject/gtmpvc.output sysname Linux hostname fmri15 machine x86_64 user crawforda vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 20 avail.processors, using 1 Creating output directory subject/gtmpvc.output Loading seg for gtm subject/mri/gtmseg.mgz Loading seg ctab subject/mri/gtmseg.ctab Reading subject/mri/gtmseg.lta Replacing 18 Pruning ctab Checking tissue type done with seg vol maxFWHM = 2.95567 (voxels), PadThresh=0.0001, nPad=10 Computing auto mask Automask, reducing FOV region 256 256 109 reduced to 21 11 3 235 245 106 ERROR: LTAconcat(): LTAs 0 and 1 do not match LTA 0 ------------------- type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 10000.0000 1 4 4 9.999997615814209e-01 0.000000000000000e+00 -8.381903171539307e-09 -7.629394531250000e-06 7.450580596923828e-09 9.999998807907104e-01 0.000000000000000e+00 0.000000000000000e+00 -7.450580596923828e-09 7.450580596923828e-09 9.999998211860657e-01 -1.525878906250000e-05 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999999403953552e-01 src volume info valid = 1 # volume info valid filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = 4.125000000000000e+00 3.554792785644531e+01 -2.000000000000000e+01 dst volume info valid = 1 # volume info valid filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = 4.125000000000000e+00 3.554792785644531e+01 -2.000000000000000e+01 subject subject fscale 0.150000 LTA 1 ------------------- type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 10000.0000 1 4 4 9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00 -2.099999237060547e+01 0.000000000000000e+00 9.999999403953552e-01 0.000000000000000e+00 -1.100000762939453e+01 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -3.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = ../CTPET/PET.template.nii.gz volume = 256 256 109 voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.029999971389771e+00 xras = -1.000000000000000e+00 -0.000000000000000e+00 0.000000000000000e+00 yras = -0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 zras = -0.000000000000000e+00 -0.000000000000000e+00 1.000000000000000e+00 cras = 3.660461425781250e+00 1.723927307128906e+02 1.247645019531250e+03 dst volume info valid = 1 # volume info valid filename = volume = 235 245 106 voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.029999971389771e+00 xras = -1.000000000000000e+00 -0.000000000000000e+00 0.000000000000000e+00 yras = -0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 zras = -0.000000000000000e+00 -0.000000000000000e+00 1.000000000000000e+00 cras = -1.861288452148438e+01 1.840597229003906e+02 1.250690063476562e+03 -------------------------- Data load time 10.9 sec nmask = 3714389, nsegs = 100, excluding segid=0 FWHM: 6 6 6 Std: 2.54797 2.54797 2.54797 nPad 10, PadThresh 0.0001 Checking Ref Ids Segmentations used for rescaling 174 Pons Computing Seg PVF Segmentation fault (core dumped) Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Fwd: One hemisphere recon-all ERROR
by Alina Rojas 20 Jul '20

20 Jul '20

External Email - Use Caution Hello Freesurfer community, I was wondering if you could look at the e-mail below. Thank you! Alina > Anfang der weitergeleiteten Nachricht: > > Von: Alina Rojas <alinacolora(a)gmail.com> > Betreff: One hemisphere recon-all ERROR > Datum: 13. Juli 2020 um 15:25:18 MESZ > An: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > > Hello Freesurfer community, > > I'm attempting to compare the cortical thickness of one side of the brain between stroke subjects. I got "ERROR: you must include rh white and pial surfaces“. I used recon-all -sd ${TARGET_FOLDER} -subjid $SUBJECTID -i $T1 -T2 $T2 -qcache -all -3T -T2pial -lh. I attached the recon-all.log file. Ist it a way to get the aparc? > > Thank you for your help, > > Alina Rojas > >

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Right and left on MRI scan and on images
by Cibele Bandeira 20 Jul '20

20 Jul '20

External Email - Use Caution Hello, I have an MRI sample collected on a Siemens Magnetom Spectra 3T scanner. However, we do not place any pointing devices inside the scanner to indicate which side is the right and which is the left. I was wondering how the images were acquired - from the front of the individuals, meaning that the left in the image is the right in the patient? Or otherwise? When processing the T1-weighted images on Freesurfer, I also have a doubt... the DICOM images are synchronized? Left in DICOM is left in the patient? And after freesurfer preprocessing? It flips the images or not? Thank you very much! -- *Cibele Edom Bandeira* Doutoranda em Genética e Biologia Molecular (PPGBM) Universidade Federal do Rio Grande do Sul (UFRGS)

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Converting volume to icosahedron surface
by Tse, Teresa 18 Jul '20

18 Jul '20

External Email - Use Caution Hi all, I am trying to convert a volume file (fMRI data in nifti format) into an icosahedron (4th order) surface using Freesurfer's mri_vol2surf command. I have been using nipype as a wrapper for Freesurfer and the other packages that I need for my processing. The command that nipype ran is: mri_vol2surf --hemi lh --icoorder 4 --o /dev/shm/RT_processing/_hemi_lh/to_surface/lh.003-FunctionalCMRR-2mm69sl1p5s_mcf.mgz --reg /dev/shm/RT_processing/convert_xfm/InplanetoAnatomy.xfm --projfrac-avg 0.000 1.000 0.100 --mov /dev/shm/RT_processing/motion_correction/003-FunctionalCMRR-2mm69sl1p5s_mcf.nii.gz --trgsubject ico The output of this command is a mgz file (attached to this email). I was unable to view this mgz file using Freeview's "Load surface" (I get the error "freadFloat: fread failed"). I was able to load the mgz file into Matlab using the load_mgh function. It loaded as a 2562 length vector (consistent with the number of vertices of a ico-4 surface). I have several questions regarding the output of the mri_vol2surf command that was run. 1) I am unsure as to whether the command that was used is correct, and whether the output mgz file that I got is the correct or expected output. What do the values of the vector represent? 2) Do you know how to load and view the output mgz file in Freeview? Is it supposed to be an overlay or annotation to an ico-4 surface file? If so, where would I find this ico-4 surface? 3) How do I find documentation and information about the icosahedron surface in Freesurfer? Many thanks, Teresa

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rtview - loading a tcl file
by Nasr, Shahin,Ph.D. 17 Jul '20

17 Jul '20

Hi Surfers, I was wondering if there is a way to load a tcl file with rtview command. Specifically, I need to change the color table to RYGB, remove the aparc, ... . Thanks

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FreeSurfer 7.1 patch question
by Dincer, Aylin 17 Jul '20

17 Jul '20

External Email - Use Caution Hi FreeSurfer Experts, Is there a tentative date when the FreeSurfer 7.1 patch and docker implementation is going to be released? Thanks! Aylin _____________________________ Aylin Dincer Senior Research Technician NeuroImaging Laboratories Imaging Core, Benzinger Lab 314-362-3629 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 1

Re: [Freesurfer] freeview 3.0
by fsbuild 17 Jul '20

17 Jul '20

External Email - Use Caution I don’t see freeview directly linking against libXm.so from Motif, though it does link against X windows libraries like libXmu.so and libX11.so.  You can see this with the “ldd” command  (some examples in screenshot below).   I don't think the RPM installer for freesurfer installs any Motif libraries.  I don't have any Motif libraries installed on my CentOS 7.7 image running under WSL that runs freeview/freesurfer. Now it could be you installed some packages on your system that installed Motif and/or also maybe changed the X windows distribution libraries (as used by freeview). - R.. On Jul 9, 2020, at 12:54, Xiaomin Yue <yuexm(a)hotmail.com> wrote:        External Email - Use Caution        Hi, Here is the command I used in the freeview 3.0: freeview – f $SUBJECTS_DIR/LOO/surf/lh.inflated.    lh.inflated was created using FS7.1.  The freeview display is attached in this email.  The inflated brain is displayed correctly when I run the same command in freeview 2.0. (see attached).   Thanks,Xiaomin From: fsbuildSent: Thursday, July 9, 2020 1:56 AMTo: freesurfer@nmr.mgh.harvard.eduCc: yuexm@hotmail.comSubject: Re: [Freesurfer] freeview 3.0         External Email - Use Caution        Hello Xiaomin, It might help for you to send along an example freeview command and file that demonstrates this issue in the WSL environment. - R.  On Jul 8, 2020, at 12:08, Xiaomin Yue <yuexm(a)hotmail.com> wrote:         External Email - Use Caution         Dear all, The Freeview (3.0) coming with fs 7.1 can not show any surface brain (inflated, pial, white) in a solid color.  The Freeview is currently running under WSL and was running without a problem until I updated libXm4.  Is there a particular library file associated with libXm4  the Freeview needs to run without this problem? ThanksXiaomin_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <freeview2_inflated.jpg><freeview3_inflated.jpg>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Fwd: question regarding mri_vol2label
by Julie Ottoy 17 Jul '20

17 Jul '20

External Email - Use Caution Hi Freesurfer team I am trying to convert parcellation (cortical) volumes that I acquired through another platform into surface labels using freesurfer. I tried following code to convert the volume with ID 20 from the parcellationvolumes.nii.gz file into a label mri_cor2label --i dir/parcellationvolumes.nii.gz --id 20 --l dir/20.label Although the code runs fine and finishes successfully, whenever I try to open the created label in freeview, it says that the label is empty. Any idea what I am doing wrong? Do you have an easier way to project all ROI volumes onto the surface? A second related question: I have run the recon-all for T1 of the subject and it creates rh.pial and lh.pial. I was wondering whether the transformation to go from T1 volume to the surface is saved somewhere and whether I can apply this transformation to convert my cortical volume parcellations into surface parcellations? Thank you for your help! Best regards Julie

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Extracting PET Binding Values from Inflated Surface
by O'Dell, Ryan 17 Jul '20

17 Jul '20

External Email - Use Caution Hi Doug, I have a question surrounding our attempts to extract PET binding values (BPND/DVR) which have been first transformed into FS subject space, mapped to the cortical surface using mri_vol2surf (signal averaged over the middle 80% of the cortical ribbon), and then displayed on the inflated hemisphere surfaces. We would like to extract the average binding values from the cortical surface ROIs using the Desikan-Killiany atlas, but are unsure how to go about this. Is there a simple way to use aparcstats2table or a similar command to extract average values from surface ROIs as defined by the ?h.aparc.annot file? Thanks! Ryan O'Dell MD/PhD PGY4 Psychiatry Resident, Yale University

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