Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

perl & bbregister conflicts
by GREGORY R KIRK 08 Nov '16

08 Nov '16

Hi folks, somebody stuck me with Ubuntu 16 for a month and I found the perl problem and so switched to the dev version which solved that problem. discovered that with the dev version bbregister throws an error having to do with fsl flirt throws an error `terminate after throwing an instance of NEWMAT::SingularException the version of fsl i have installed is 5.0 of course so i use dev for recon and 5.3 for bbregister so just to let you know the bbregister/fsl problem is there in the latest dev cheers Greg

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Qdec plot design
by Mihaela Stefan 07 Nov '16

07 Nov '16

Hello Freesurfers, I am doing a group analysis using Qdec. I have a few significant clusters and I would like to plot one of them. Qdec does that if I click on 'Find Clusters and Goto Max' but I don't see options for the design of the plot. How can I export the thickness values from my cluster to reproduce the Qdec plot in another program? Thank you! Mihaela

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MRI Freesurfer
by Daniel Alejandro Reyna Torres 07 Nov '16

07 Nov '16

Hello, my name is Daniel Reyna, I am currently working with Freesurfer to analyse the cortical segmentations and parecellations that the program outputs. I have analysed some MRI but I am not sure whether I have achieve best results or probably there is something I should improve. One question is the input type. I have used dicom files but, the type of MRI should it be an axial or sagital view, or any? It seemes that Freesurfer accepts either type of MRIs, I just wanna be sure that the program is contioned for those type of MRIs. Second, is there any special recommendation for the quality or characteristics of the MRI?, i.e., the number of layers per each 3D MRI, resolution, size of voxel ... I ask this so I can ask the labs for specific conditions to maximise results with the reconstruction in Freesurfer. I currently receive images from several labs, they have different protocols for making the brain scan. I´ve been told that I could ask them for "special conditions" if that is the case. Thank you very much! Best regards, Daniel Reyna

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Cortical white matter
by Del Re, Elisabetta 07 Nov '16

07 Nov '16

Dear FreeSurfer team, does the cortical white matter volume include the cerebellum? Thank you, regards, Elisabetta

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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

1 0

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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