Freesurfer

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30081 discussions

Unsupported slice timing pattern 5 in version 5.3.0
by Leonardo Tozzi 06 Jul '16

06 Jul '16

To Whom it may concern, I have tried to run the recon-all pipeline on some T1 data and have encountered the following error: nifti1Read(): unsupported slice timing pattern 5 I have browsed the previous threads about it and it appears that it should have been fixed in version 5.3 but that is the version I run and the error is still there. The data has been converted to NIFTI from DICOM using MRIcron and I don't have access to the original DICOMs. I have seen that someone posted a modified version of nifti1Read() in the past and I was wondering if it was still available. I am running Freesurfer 5.3.0 on MacOSX El Capitan 10.11.3. Would you have any suggestions on how to proceed? Thank you very much. Yours faithfully, Leonardo Tozzi, MD PhD Student Trinity College Institute of Neuroscience College Green, Dublin 2 Ireland

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Not able to find file in gtmseg
by Lee Subin Kristine 06 Jul '16

06 Jul '16

Dear FreeSurfer experts, Hello, I am trying to use Freesurfer's (developmental version) PVE correction tool and I haveone question. The data to be PVE-corrected are some preprocessed PET data downloaded from the Alzheimer's DIsease Neuroimaging Initiative (ADNI) database. Basiclly, the dynamic PET images have been co-registered to one another, averaged, and spatially normalized to a common space. Now I am trying to apply PVE-correction. It seems from your answers here (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html)<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html>that you run the following commands: (1) gtmseg (2) bbregister (3) mri_gtmpvc (4) mri_glmfit When I enter gtmseg --s subject such as below ('Desktop/forFSsubin_2' is location of the subject MRI and '019_S_4835_N3m_cub_ACPC.nii' is the filename) ~/Desktop/forFSsubin_2$ gtmseg --s 019_S_4835_N3m_cub_ACPC.nii I get: ERROR: cannot find 019_S_4835_N3m_cub_ACPC.nii I have changed directory to the folder where the subject MRI file is, and I have typed the subject's filename correctly, but it keeps saying the subject file cannot be found. Any ideas on what is wrong here? Any help would be appreciated. Thank you in advance. Regards, Subin

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convert from MNI152 to native space
by Leila Reddy 06 Jul '16

06 Jul '16

Hi, I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in Freeview: mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o mask_in_Native.nii --mni152reg The overlay of the mask on f.nii in Freeview is mostly outside the brain. How can I go about this step? Thanks for your help,Leila

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Hippocampal subfields segmentation - what is the voxel size of the input?
by Fernando Pasquini Santos 06 Jul '16

06 Jul '16

Dear, I have a doubt regarding the input T1 image used for the Hippocampal Subfield segmentation in Freesurfer 6.0 - https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields In this documentation it says that I can use a standard 1mm T1 image or the same standard 1mm T1 image with an additional scan. However, I want to use a 0.7mm T1 image as input, with an additional T2 scan. When I run the program with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel size. So, I don't know if this happens just because of the recon-all program or if the segmentation is being done in the downsampled T1 image or in the original 0.7mm. By reading the article "A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI" I saw that, in the methods section, the algorithm is used to segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? Obviously, doing the segmentation directly on 0.7mm data would be better than a downsampled version to 1mm... Thanks, Fernando Pasquini Santos PhD student in Dynamic Systems fernandosantos(a)pitt.edu fernando.pasquini.santos(a)usp.br

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hippocampal subfields command
by Alexopoulos, Dimitrios 06 Jul '16

06 Jul '16

A quick question re: hippocampal segmentation. I have processed 1mm isotropic T1 data with 5.3 using the following command: recon-all -qcache -all -hippo-subfields How is this this different than using the following command I have found here: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields -hippocampal-subfields-T1 Thanks. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email.

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segmentation issues in Temporal Lobes
by Barbara Kreilkamp 06 Jul '16

06 Jul '16

Dear Freesurfers, Unfortunately I am having a problem with recon-all segmentation in some of my participants. It seems that part of the brain is cut off in the medial part of the Temporal lobes (please see attachment), around the region where the hippocampus is. I am unable to place WM region control points, as the algorithm does not have seemed to miss white matter, rather only gray matter of the hippocampus. I've seen on your website that also there the cortical surface does not include the hippocampus, so I wonder if this is intentional? Problem is that the surface here grasps some of the hippocampus but not all of it. What is the best way of solving this? Thanks very much. Best wishes, Barbara

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Inquiries about the curvature
by Mahtab Farahbakhsh 06 Jul '16

06 Jul '16

Dear FreeSurfer, I am using the mris_anatomical_stats output to calculate the curvature and thickness indices for different brain areas. However, I am not sure what the mean and gaussian curvatures mean. I could not find a complete description on these two. Would you please guide me what principle curvature and mean and gaussian curvatures means exactly? I appreciate your concern in advance. Best Regards, Mahtab.

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Re: [Freesurfer] Freesurfer/Freeview help
by Abbie McNulty 06 Jul '16

06 Jul '16

Hello, Just a couple more questions that would be great if you could answer in explanation form: How do people develop finite element models from brain MRI? How do people learn and implement the software on an example data set? Abbie On Tue, Jul 5, 2016 at 9:42 AM, Abbie McNulty <amcnult1(a)stanford.edu> wrote: > Hello, > > Just a couple more questions that would be great if you could answer in > explanation form: > > How do people develop finite element models from brain MRI? > How do people learn and implement the software on an example data set? > > Abbie > > On Mon, Jun 27, 2016 at 6:37 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > >> Hi Abbie >> >> you just use the recon-all script from the command line: >> >> recon-all \ >> -i <path to 1 file in the correct dicom series> \ >> -sd <path to the directory that you store all your subjects> \ >> -s <identifier to give this subject> \ >> -all >> >> this will take 5-20 hours and at the end will create and populate a >> directory tree with segmented volumes and surfaces >> cheers >> Bruce >> >> On Mon, 27 Jun >> 2016, Abbie McNulty wrote: >> >> > Hi Bruce, >> > I am trying to create a mesh of the MRI scans, eventually with imported >> > scans, but for now just using the information available through the >> > software. How do you work these voxel segmentations? I'm just very new >> with >> > the software. >> > >> > Say I import an MRI scan, and I want to cortically segment it in order >> to >> > create a mesh of the volume. What are the steps to do this and how do I >> > follow through with each step? I tried to watch the youtube tutorials >> on the >> > Freesurfer youtube, but since they are slides informing of what >> Freesurfer >> > can do and not quite a play-by-play interaction of Freeview, I am stuck. >> > >> > Thanks >> > >> > Abbie >> > >> > On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl < >> fischl(a)nmr.mgh.harvard.edu> >> > wrote: >> > Hi Abbie >> > >> > what are you trying to create a mesh of? We supply meshes for >> > the >> > gray/white interface and for the pial surface. We supply voxel >> > segmentations of lots of other things that you could mesh, but >> > we don't >> > by default. >> > >> > cheers >> > Bruce >> > On Mon, 27 Jun 2016, Abbie McNulty wrote: >> > >> > > Hello, >> > > I am trying to segment a MRI brain in order to create a mesh >> > of the image >> > > into finite elements, but I am very new with >> > Freesurfer/Freeview and am not >> > > familiar with the tools. So far, I have only uploaded >> > brain.mgt from the >> > > bert file that comes with the program. If I wanted to mesh >> > this brain, how >> > > should I proceed? The online tutorials have confused me >> > especially since I >> > > am not sure if I am supposed to be using the terminal or the >> > command window >> > > for a lot of the code commands. >> > > >> > > Any help would be appreciated. >> > > >> > > Thanks! >> > > >> > > Abbie McNulty >> > > >> > > -- >> > > Abigail C. McNulty >> > > Stanford University Class of 2018 >> > > B.A. Candidate in Bioengineering >> > > Stanford Women's XC/ Track and Field >> > > >> > > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > The information in this e-mail is intended only for the person to whom >> > it is >> > addressed. If you believe this e-mail was sent to you in error and the >> > e-mail >> > contains patient information, please contact the Partners Compliance >> > HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was sent to you >> > in error >> > but does not contain patient information, please contact the sender >> > and properly >> > dispose of the e-mail. >> > >> > >> > >> > >> > -- >> > Abigail C. McNulty >> > Stanford University Class of 2018 >> > B.A. Candidate in Bioengineering >> > Stanford Women's XC/ Track and Field >> > >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > > -- > Abigail C. McNulty > Stanford University Class of 2018 > B.A. Candidate in Bioengineering > Stanford Women's XC/ Track and Field > -- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field

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FSFAST time series extraction
by curry_sam77＠yahoo.com 06 Jul '16

06 Jul '16

Hi all, I am trying to extract mean time series BOLD data using FSFAST from Cortical ROIs + sub cortical ROIs and cerebellum. preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd mri_segstats --annot fsaverage lh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt mri_segstats --annot fsaverage rh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt and for cortical time series mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf subCorticalTimeSeries.txt But I am not sure on how exactly to extract time series from cerebellar regions. So if I want to extract time series from regions as described in Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in FreeSurferCololLUT.txt? If not could you please direct me to processes that I can use. Sent from Yahoo Mail. Get the ap

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mri_surfcluster
by tom parker 06 Jul '16

06 Jul '16

Dear Freesurfers, I ran a comparison between different groups using mri_glmfit. Now I would like to correct the results in sig.mgh by multiple comparisons using FDR. I tried using tksurfer but it doesn't work so well on my computer and I read that freeview does not allow to do that yet. I'm now trying to use mri_surfcluster to do it. Is this correct? mri_surfcluster --in sig.mgh --subject fsaverage --surf inflated --hemi lh --fdr 0.05 --sign pos After I run it some thresholds appear in the terminal. Should I use these thresholds to create a FDR corrected sig.mgh map or is there a direct way of getting this using mri_surfcluster or other command? Thank you so much!

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