Freesurfer June 2019

freesurfer@nmr.mgh.harvard.edu

82 participants
138 discussions

Re: [Freesurfer] How to get the difference between orig.mgz and original image
by chen 09 Jun '19

09 Jun '19

External Email - Use Caution Hi Bruce, Thanks for your reply. I appreciate your help a lot! Just a simple question. How to check the ratio of amygdala in intensity in the orig.mgz with other gray matter? I am looking forward to your suggests. Cheers, Jiachen

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transformation from volume to surface
by Yamada, Takashi 08 Jun '19

08 Jun '19

External Email - Use Caution Hi there, I try to transform from volume-based ROI mask (nifty file) to suface-based file. I input the following. mri_vol2surf --mov (volume.nii) --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --0 (output.mgh) Then, mri_info tells me 134583 dimesions. However, I cannot overlay this mgh file on the lh.inflated. freeview -f lh.inflated:overlay=.../output.mgh How should I do? Best regards, Takashi Yamada --------------------------------------------------------------------------------------------------------------------- Takashi Yamada, MD & PhD Postdoctorial Research Associate Department of Cognitive, Linguistic and Psychological Sciences (CLPS) Brown University Box 1821 190 Thayer Street Providence, RI 02912 TEL : +1 401 863 9488 FAX : +1 401 863 2255 Email: takashi_yamada(a)brown.edu --------------------------------------------------------------------------------------------------------------------------------

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Uncorrected cluster information
by Pedro Rosa 08 Jun '19

08 Jun '19

External Email - Use Caution Dear all, I would like to obtain information regarding clusters yielded by GLM group analysis before correction for multiple comparisons (hence uncorrected). I used tksurfer to look at the clusters (sig.mgh) and was able to apply statistical thresholds, but could not obtain further information from them (as available in the .summary file after correction for multiple comparisons, such as mean cluster value, cluster size). Can you help me? Many thanks in advance, Pedro.

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Longitudinal edits
by Sierra Ann Jarvis 08 Jun '19

08 Jun '19

External Email - Use Caution Hello freesurfer, I am having a difficult time organizing my command to apply the Pial edits that I have made to my .longs. The bases came out just fine but the .longs needed Pial editing. Here is what I have tried but I still get errors. recon-all -long C002d C002d.long.C002.base -mprage -3T -norm2-b 20 -norm2-n 5 -autorecon2 -autorecon3 C002d is the cross-sectional. I also tried putting the base in this position as well and it still created an error. I am unsure of how what the command is and have read through: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits <https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits> Still no luck on how to properly organize this command. Any help or guidance would be greatly appreciated, -Sierra Jarvis

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A Question about fcseed-config in larger parcellation
by Sara Jafakesh 07 Jun '19

07 Jun '19

External Email - Use Caution Dear FreeSurfer experts, I want to calculate functional connectivity analysis with 400 parcel, we divided the parcellation with "mirs-divide-parcellation" before, now I want to know when I use "fcseed-config" to obtain the seed signal, how can I set the id (with segid flag)? I mean how can I use and set my manual lookup table with 400 parcel instead of FreeSurfer-lookup table? "$FREESURFER_HOME/FreeSurferColorLUT.txt" I would be grateful if you could help me. Best regards, Sara,

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Re: [Freesurfer] T2/Flair benefits in freesurfer 6.0
by Glasser, Matthew 07 Jun '19

07 Jun '19

External Email - Use Caution Higher the better resolution, but it's particularly important that the resolution is close to 3D isotropic for surface reconstruction. Matt. On 6/7/19, 1:38 PM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Jones, Richard" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of richard.jones(a)choa.org> wrote: External Email - Use Caution A few more questions regarding the use of a FLAIR image. 1)If one is using the hires option on T1 images acquired with sub-millimeter spatial resolution then, to get the best results with the FLAIR option, is matching spatial resolution required for the FLAIR sequence? 2)In a post some time ago (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51413.html) you said "V6 was not meant for T2/FLAIR and we didn't test it extensively. We have been optimizing things in the past week for T2/FLAIR and I expect 6.1 will be better for them". Are the changes you were referring to incorporated in the current development version? 3)Are then any plans to use the FLAIR for multi-modal segmentation in order to refine the segmentation of the Pallidium and Putamen, and to possibly segment structures such as the substantia nigra and red nucleus? Thanks, Richard Date: Tue, 4 Jun 2019 12:41:51 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2/Flair benefits in freesurfer 6.0 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1906041241290.302(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Aaron yes, it helps in other situations like blood vessels cheers Bruce On Tue, 4 Jun 2019, Aaron Tanenbaum wrote: > > ????????External Email - Use Caution???????? > > I am not too sure if I have asked you this question before. I know the use > of a flair or T2 helps with dealing with the dura. I was wondering if there > are other benefits?? > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ________________________________ 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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Re: [Freesurfer] T2/Flair benefits in freesurfer 6.0
by Jones, Richard 07 Jun '19

07 Jun '19

External Email - Use Caution A few more questions regarding the use of a FLAIR image. 1) If one is using the hires option on T1 images acquired with sub-millimeter spatial resolution then, to get the best results with the FLAIR option, is matching spatial resolution required for the FLAIR sequence? 2) In a post some time ago (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51413.html) you said "V6 was not meant for T2/FLAIR and we didn't test it extensively. We have been optimizing things in the past week for T2/FLAIR and I expect 6.1 will be better for them". Are the changes you were referring to incorporated in the current development version? 3) Are then any plans to use the FLAIR for multi-modal segmentation in order to refine the segmentation of the Pallidium and Putamen, and to possibly segment structures such as the substantia nigra and red nucleus? Thanks, Richard Date: Tue, 4 Jun 2019 12:41:51 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2/Flair benefits in freesurfer 6.0 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1906041241290.302(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Aaron yes, it helps in other situations like blood vessels cheers Bruce On Tue, 4 Jun 2019, Aaron Tanenbaum wrote: > > ????????External Email - Use Caution???????? > > I am not too sure if I have asked you this question before. I know the use > of a flair or T2 helps with dealing with the dura. I was wondering if there > are other benefits?? > >

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error matlab segmentHA
by stdp82＠virgilio.it 07 Jun '19

07 Jun '19

External Email - Use Caution I have installed matlab 2018b and removed 2014b. When I run segmentHA_T1.sh the error reported below occurs: MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37:3955 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args Darwin iMac-di-Stefano.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Apr 24 21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at Tue Jun4 00:55:25 CEST 2019 For more details, see the log file /Applications/freesurfer/subjects/subj/scripts/hippocampal-subfields-T1.log Please also take in account segmentation violation detected at Tue Jun4 00:57:53 2019 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root: /Applications/freesurfer/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) MATLAB Version : 8.4.0.150421 (R2014b) Why it does not find 2018 version? I have follow the guidelines at https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime Thanks Stefano

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CSF MASK
by Marina Fernández 07 Jun '19

07 Jun '19

External Email - Use Caution Dear Freesurfer experts, Is there any way to obtain a CSF mask in Freesurfer similar to that obtained with the SPM segmentation (see attached)? Thank you in advance. Best regards, Marina.

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scan acquisition date from recon all
by Boris Rauchmann 07 Jun '19

07 Jun '19

External Email - Use Caution Dear all, is there any way to find the scan acquisition date in the recon-all log? Thanks, Boris

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Freesurfer June 2019