Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

a retinotopy question
by Xiaomin Yue 07 Nov '16

07 Nov '16

Hi All, During the experiment, a wedge was presented clockwise, starting from the low vertical meridian, and a ring was presented from center to peripheral. The analysis done successfully with fs5.3 generated values of polar angle and eccentricity for each voxel. For example, the voxel A has polar: 1.79, and eccen: 4.8. From those values, can I determine where in the visual field the voxel A represent? If so, how? Thanks, Xiaomin

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Re: [Freesurfer] Freesurfer Digest, Vol 153, Issue 8
by Daniele Orlandi 07 Nov '16

07 Nov '16

Ciao Eugenio, I've just checked the presence of the file T1resampled.mgz and it doesn't show up in tmp/ folder as well as in other folders of the same subject. Morover, the T1resampled.mgz file is not present in ever subjects folder at every time point as well as for the base/template folder. Daniele Message: 11 Date: Mon, 7 Nov 2016 16:47:02 +0000 From: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Subject: Re: [Freesurfer] FreeSurfer 6.0 (beta) Error in segmentSubjectT1_autoEstimateAlveusML (line 588) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <AED2F588-0F26-4361-BEA8-3162D0A861A9(a)ucl.ac.uk> Content-Type: text/plain; charset="utf-8" Ciao Daniele, This is weird. Would you mind verifying that file T1resampled.mgz actually exists in the temporary directory of the subject? You can do that by CDing to $SUBJECT_DIR/[SUBJECT_NAME]/tmp and running the command: find . -name ?T1resampled.mgz? Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 7 Nov 2016, at 16:39, Daniele Orlandi <dorlandi(a)fatebenefratelli.eu<mailto:dorlandi@fatebenefratelli.eu>> wrote: Dear experts, I've finished FSv5.3 longitudinal analysis and I'm now running FSv6.0(beta) for hippocampal subfield features extraction (always on Ubuntu 14.01 environment). After several trial I realized that before pipeline ends I've got the following error: /opt/FreeSurfer-6-Beta/bin//mri_mask -T 0.5 T1resampled.mgz hippoMaskResampledDilated.mgz T1resampled.mgz >/dev/null: Signal 127 Error using kvlGEMSMatlab /cluster/koen/eugenio/GEMS/itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x7fe88bcda050): Can't find/open file: T1resampled.mgz Error in kvlReadCroppedImage (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 588) Could you help me? Best Daniele PS: Even though one of the last row display " finished without error", no output is generated in the /mri/ folder. -- -- Daniele Orlandi, PsyD IRCCS Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel: +39 030 35 01 563 e-mail: dorlandi(a)fatebenefratelli.eu<mailto:dorlandi@fatebenefratelli.eu> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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.

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FreeSurfer 6.0 (beta) Error in segmentSubjectT1_autoEstimateAlveusML (line 588)
by Daniele Orlandi 07 Nov '16

07 Nov '16

Dear experts, I've finished FSv5.3 longitudinal analysis and I'm now running FSv6.0(beta) for hippocampal subfield features extraction (always on Ubuntu 14.01 environment). After several trial I realized that before pipeline ends I've got the following error: /opt/FreeSurfer-6-Beta/bin//mri_mask -T 0.5 T1resampled.mgz hippoMaskResampledDilated.mgz T1resampled.mgz >/dev/null: Signal 127 Error using kvlGEMSMatlab /cluster/koen/eugenio/GEMS/itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x7fe88bcda050): Can't find/open file: T1resampled.mgz Error in kvlReadCroppedImage (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 588) Could you help me? Best Daniele PS: Even though one of the last row display " finished without error", no output is generated in the /mri/ folder. -- -- Daniele Orlandi, PsyD IRCCS Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel: +39 030 35 01 563 e-mail: dorlandi(a)fatebenefratelli.eu

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Email address
by Meysam Ebrahimi 04 Nov '16

04 Nov '16

Master.msa75(a)gmail.com

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mris_preproc
by Alshikho, Mohamad J. 04 Nov '16

04 Nov '16

Dear FS experts, I ran surface based analysis using PET maps, and the pipeline reported, in FS list, by multiple colleagues as the following: * spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh * mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat ..... --projfrac 0.5 --out lh.mgh * mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh * mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir// * then mri_glmfit-sim to correct for multiple comparison. I wanted to know the correct usage of the flag "projfrac" in the command "mris_preproc": My understanding is that this flag control running the surface based analysis far from the surface (i.e. close to the surface or deep in the white matter) * If it is 0.5 ==> that means the surface based analysis is running in the middle area between white and pial * if it is zero ==> the surface based analysis is running close to white matter * if it is +1 ==> that means the surface based analysis is running close to the pial * if it is -1 ==> that means the surface based analysis is running deep in the white matter Kindly: 1. Is this correct? 2. Can I use values like -2 or -3 ... etc to run the analysis deep in the white matter. I aim to run surface based analysis on multiple layers of the brain deep from the pial to investigate how the PET signal is going to change between these layers? 3. What is the difference between the flag "projfrac" and the flag "projdis" 4. If I replace the PET maps in the previous pipeline by diffusion maps? Is it keep valid for diffusion data? Many Thank! Mohamad

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CUDA 8.0 and error on recon-all nu_correct
by anonymous anonymous 04 Nov '16

04 Nov '16

Hi all, I'm new to freesurfer and I'm having some issues. 1) First of all I tried recon-all in one subject but I got an error on nu_correct. This is what the log says: Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct I searched through the mail list and I found that it may be because my data is in an external hard drive... (the hard drive is in FAT32). But it's not because the data is in the external hard drive. I copied a folder to my computer and I got the same problem. Could it be the data? 2) Then I tried to install CUDA 8.0 ... I don't know if succesfully because the command cudadetect shows the following: cudadetect.bin: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Reading as well I'm afraid that freesurfer may not be able to use versions of CUDA that are +5? I have an NVIDIA Geforce GTX 950 and using NVIDIA binary driver version 370.28. 3) I think after the installation of CUDA using a .deb I got the paths messed up and now I can't even use recon-all on my hard drive. When I type recon-all on any other external hard drive or folder, it does show the information though. I dont know if it's a permissions problem (I also had a blackout earlier...) but the hard disk's files and folders seem to have all permissions and the ownership is root:root. I can't remount it now because I'm running some things using fsl... Please any help would be really appreciated. I've spent a loooot of hours struggling with all these. I'm on a ubuntu 16.04 by the way. Thaaaaaankius

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mapping ROI to surface space
by Andrews, Derek 04 Nov '16

04 Nov '16

Hello Freesurfer Developers and Community, I am looking to map a ROI.nii based on the MNI152 template to the fsaverage pial surface. I have used the following commands Bbregister -s fsaverage -mov MNI152.nii -reg register.dat -init-fsl -12 -t1 Then mri_vol2surf -src ROI.nii -out ROI.mgh -srcreg register.dat -hemi lh The ROI appears to be in the right place however is very blotchy. Have I missed a step? Or is this correct? See bellow a picture of the ROI highlighted in FSL and in tksurfer after mapped using the above. Thank you for your support, Best, Derek [cid:20AF047A-6501-433B-9BE0-F5410F5ED296] ________________________________ Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews(a)kcl.ac.uk

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ROI NumVert
by Daya P 04 Nov '16

04 Nov '16

Hi All, My question is about using mri_label2label. When mapping the labels from one subject to another the number of vertices of each ROI is different. Is that something to be expected? How much of a difference does a number of vertices of 50 compare to 40 have on measures like thickness, grey matter and surface area? I would really appreciate some help Thank you, Daiana R. Pur Research Assistant Canadian Surgical Technologies & Advanced Robotics Brain and Mind Institute Western University London, ON, N6A 5B7 Canada

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Registration
by Robert Kraft 03 Nov '16

03 Nov '16

My ultimate goal is apply the CVS transforms to ROIs (similar to aseg.mgz) that are defined in MNI space to anatomical space. Unfortunately, I am having trouble doing this. As a start I am trying to transform my T1w image to MNI space. My understanding so far is that I need to do the following 1) Perform mri_cvs_register to generate the transforms. 2) Then apply the transform using mri_vol2vol I have been able to perform the mri_cvs_register step with the following commond nohup mri_cvs_register --mov s001 --mni --nocleanup > nohup.mri_cvs_register & This worked fine and generated the expected output. The el_reg_tocvs_avg35_inMNI152.mgz overlay with the MNI152 space nicely. As a test of my understand I apply the tm3d transform to the to the original brain.mgz image to see if I can transform the original volume to MNI space. I did this with the applyMorph command applyMorph --template MNI152_T1_1mm_brain.nii.gz --transform el_reg_tocvs_avg35_inMNI152.tm3d vol ../mri/brain.mgz mni.brain.mgz linear This worked well and the results are what I expected. Now what I would like to do is do the inverse transform the MNI template into the conformed native space. The applyMorph doesn’t appear to have an inverse capability but mri_vol2vol does. I tried to apply does. In order to understand how the mri_vol2vol command works I transformed the brain.mgz into MNI space with mri_vol2vol with the following command mri_vol2vol --mov ../mri/brain.mgz --targ MNI152_T1_1mm_brain.nii.gz --m3z combined_tocvs_avg35_inMNI152_elreg_aseg.m3z --o vol2vol_mni_brain.mgz --noDefM3zPath --interp trillion This didn’t work. It is clear that I am not applying the correct affine transformation matrix first. The mri_cvs_register produces a transform.txt file containing 1.02826 -0.0139273 0.091057 0.0115285 0.990443 -0.222876 -0.0255966 0.234528 0.949605 -3.40075 3.35495 30.3486 However, I am not sure how to incorporate this into the mri_vol2vol function. There are lots of options for the specifying the affine transformation file but the transform.txt doesn’t seem to be in the right format. Frankly, I am just guessing to do from here. I would appreciate any advice or links to documentation. I would also like to know what is the relationship and/or difference between mri_vol2vol and the applyMorph function. Why is there a need for both? When is it appropriate to these functions that seem to do very similar things. Thanks for your help, Bob

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how to edit the cortex label by adding vertecies
by l.c.b.norbom＠psykologi.uio.no 03 Nov '16

03 Nov '16

Hello Freesurfer Developers, I want to add vertecies to the cortex label as certain vertecies in the occipital lobe is wrongfully segmented as medial wall. Is there a way to do this? Thank you in advance! Cheers, Linn

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Freesurfer November 2016