Freesurfer June 2016

freesurfer@nmr.mgh.harvard.edu

152 participants
213 discussions

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

3 5

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

4 9

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

3 2

Hippocampal Subfields Segmentation
by Permesh Dhillon 06 Jul '16

06 Jul '16

Hello FreeSurfer Developers, I’m having issues with the hippocampal subfields segmentation using OS X Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611. I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting an error message : Error:CTF file '/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' failed to open for 'Read' access. Error message: 'Open a zip file for read/modify failed.’ The segmented hippocampal files as described on free surfer wiki cannot be found under the subject ‘mri’ folder. I understand other users have complained of a similar issue within the last week. I’d ve grateful if you could assist me with the issue above. Many thanks Permesh This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

3 8

Any updates on recon-all GPU support?
by Derek Pisner 05 Jul '16

05 Jul '16

Anyone manage to successfully configure recon-all to run with -use-gpu for recent cuda toolkit versions? I realize cuda support has ceased over the past few years for Freesurfer, but have there been any successful builds for CUDA toolkit versions 6 and up? I am currently looking to configure cuda support on a Tesla K80 GPU, which is part of a small beowulf cluster, which is working wonderfully with FSL's cuda support. Many moons ago, when gpu support was working, I found the -use-gpu option with recon-all to be significantly faster and more practical (for the user) than the -openmp option (which even on a 150 core cluster has provided limited speedup during batch runs). Curious to hear what others have been doing. -Derek

3 20

Apply mris_apply_reg for a label
by Alexandre Routier 05 Jul '16

05 Jul '16

Hello everyone, I have a label for the left hemisphere for my subject but I don't understand the syntax to apply mris_apply_reg on this label to obtain the right hemisphere version. mris_left_right_register was performed to get lh.sphere.left_right and lh.sphere.left_right but I don't know how to use this for the mris_apply_reg command. Thanks in advance for your answer. Alexandre

3 3

Maps/seed on surafce
by Martin Juneja 05 Jul '16

05 Jul '16

Dear FreeSurfer and SPM experts, I am trying to calculate functional connectivity maps using FreeSurfer pipeline: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… . After defining a seed region on raw anatomical image, I co-registered functional data with anatomical data (as reference) and made sure that the seed is at correct place on both anatomical (top left in attached image) and functional (top right) data. Using SPM, I confirmed co-registration was fine. But after running all the steps of FC, looks like the FC maps are not correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I am not getting significant FC at seed location. Here, bottom right shows the seed location on surface after I convert the seed to fsaverage space (for visualization purpose). Any thoughts, ideas or tips on what went wrong here, would be really appreciated. Thanks.

2 3

Order of overlays
by Reza Rajimehr 05 Jul '16

05 Jul '16

Hi, In Tksurfer, we want to show functional activity map and borders of aparc on a surface. The borders of aparc are always drawn on top of the activity map, which sometimes hide small activation blobs. Is it possible to draw the activity map on top of the aparc borders? Reza

5 4

[TRACULA] ERROR: cannot unpack mosiacs without ASCII header
by Koubiyr, Ismail 05 Jul '16

05 Jul '16

Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. Thank you in advance for your help, Ismail

2 10

tracula not work
by yangfuxing 04 Jul '16

04 Jul '16

Hi professor， When I finished setting up the configuration file "dmrirc", type "trac-all -c dmrirc"in the terminal ,it return "FSLDIR: Undefined variable", how can I solve it?Thank you. Best, yang

2 1

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Freesurfer June 2016