Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30097 discussions

Cortical Thickness Processing Error
by Navena Rebecca Lingum 13 Jun '16

13 Jun '16

Dear FreeSurfer experts, I am currently in the process of running the mris_anatomical_stats command line to look at cortical thickness however, the output states that the annotation file could not be read. Please see below for command line and output: navenalingum% mris_anatomical_stats -a N1/label/lh.aparc.annot -b N1 lh computing statistics for each annotation in N1/label/lh.aparc.annot. reading volume /Users/navenalingum/Applications/freesurfer/subjects/N1/mri/wm.mgz... reading input surface /Users/navenalingum/Applications/freesurfer/subjects/N1/surf/lh.white... reading input pial surface /Users/navenalingum/Applications/freesurfer/subjects/N1/surf/lh.pial... reading input white surface /Users/navenalingum/Applications/freesurfer/subjects/N1/surf/lh.white... could not read annot file N1/label/lh.aparc.annot No such file or directory mris_anatomical_stats: could not read annotation file N1/label/lh.aparc.annot No such file or directory Could it be that there was an error in the recon-all processing stage? Your help would be greatly appreciated! Thanks, Navena Lingum

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Help resolving ERROR: Invalid FreeSurfer license key found in license file
by Suzanne Witt 13 Jun '16

13 Jun '16

Hej. I recently tried to create a license file for a Unix-based installation of FreeSurfer that previously had no license file associated with it. With the help of our IT people, I have tried copying the lines I received via email into a file named ‘license.txt’ and then following responses I found on the message board to similar problems, into a file named ‘.license’. In both cases, I get the same error: ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt or ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license I have since tried performing a completely new installation of freesurfer, recreating the .license file using a text editor (per a previous message found about this error on the message boards). I am still receiving the same invalid FreeSurfer license error message. To the best that I can figure out, there do not appear to be any sort of ‘end of line’ characters in any of the iterations of our attempts to create this license file. I have noticed many messages about this error in the archives, but none of the suggested fixes seem to be working for me. Any help at this point would be much appreciated. Thanks in advance, suzanne

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checking freesurfer output
by Gabor Perlaki 13 Jun '16

13 Jun '16

Dear all, I've a lot of patients and we are looking for the fastest solution to check the output of Freesurfer. On the troubleshooting page ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) there are a lot of steps to check, but I think not all of that should be done to find out whether there is error in the final segmentations. I think, but I am not sure, that checking the surfaces (white and pial) and checking the subcortical segmentations (aseg) is enough to realize if something is wrong. After an error is detected based on the checked outputs (surfaces and aseg), we can find out the exact nature of the error and correct it based on the troubleshooting page. Is it a good solution for verifying the performance of Freesurfer by checking only these two things (surfaces and aseg) or I need to check all of the steps listed on the troubleshooting page anyway? Best Regards, Gabor <petzinger.gabor(a)gmail.com>

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Cerebellar volumes?
by Marja Caverlé 12 Jun '16

12 Jun '16

Hi all, I am hoping to find some cerebellar volumes, but I don't know how to get them. I already did recon -all on all my subjects, but I cannot find any of these numbers in the .stats files. Am I just missing them, or does the recon all not do any cerebellar stuff? Best, Marja

3 9

converting ME-MPRAGE files
by Limachia, Gaurang (NIH/NINDS) [F] 10 Jun '16

10 Jun '16

Hello All, We have acquired our anatomical images on a Siemens scanner as multiecho MPRAGE sequence (4 echos), and wish to unpack the runs so we can perform morphometric analysis using FreeSurfer. What is the optimal way to convert the DICOM files so we can use them with FreeSurfer tools? Specifically, what command line do you recommend for dcmunpack? When running the command: dcmunpack –src dicomdir we get the following output: Found 1 unique series: 6 6 3D_T1_MEMPRAGE 7.27 2530 7 unknown ROW 650 dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm Not sure how to interpret this. Thanks. Gaurang Limachia

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BERT is not working correctly with the toolbox list below the brain
by John Mitchell 10 Jun '16

10 Jun '16

When I open freesurfer and type the command to pull up bert the brain pops up but the toolbox (icons) below it that are supposed to come up as well do not? Help is appreciated!

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Freesurfer Help
by John Mitchell 10 Jun '16

10 Jun '16

Hello, I just downloaded and installed Freesurfer and I had just a few basic questions. 1. When I type in the command to "test the installation type" using "tksurfer bert lh inflated -annotation aparc" I get the bert brain image, however I don't get the tksurfer tools popup below it with all the different icons and options and I don't know why?2. When I go to the GIMP image editor just to explore and play around with it, I selected the paint brush to draw on my selected image, however when I go to change the color from black to any other color (and it shows that I've selected a different color) it still draws/paints black on my image? Thank you for time and help!-John M.

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Re: [Freesurfer] using both T1/T2 and resolutions
by Matt Glasser 10 Jun '16

10 Jun '16

Hi Jim, I would just use the HCP Pipelines for that: https://github.com/Washington-University/Pipelines, as they take care of all of those things re FreeSurfer. I would set to using the 0.8mm templates so that nothing is down sampled. Peace, Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios" <Alexopoulos_D(a)kids.wustl.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, June 10, 2016 at 10:56 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] using both T1/T2 and resolutions Hi, We¹d like to process pediatric data through the complete FS 5.3 pipeline. The T1/T2 data are acquired with a 3T Siemens as follows: T1 mpr sag - 0.82x0.82x0.85 T2 Space - 1x1x1 We¹d like to process using both the T1 and T2 (for better dura removal and possible myelin analysis). Is it possible to use the hires T1 and have data not downsampled to 1x1x1? Ifpossible, can this be done in tandem with the lower resolution T2-space? What recon-all command would be best for this process? 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. _______________________________________________ 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.

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Brainstem Substructures does not work.
by shi yao wang 10 Jun '16

10 Jun '16

Dear FSL expert: Firstly, I would like to thank for the reply from Douglas. Thank you for your suggestion! aparcstats2table is working!. Then, I have another question about the brainstem substructures. According to the guideline, https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime I download the environment and successfully installed. However, when I running command " recon-all -s subject -brainstem-structures" it shows wrong message "ERROR: Flag -brainstem-structures unrecognized. -s 201 -brainstem-structures" So how can I fix it? Is that due to FSL version problem? If yes, how can I update to freesurfer 6.0? thanks! Lawrence Emory.

2 1

using both T1/T2 and resolutions
by Alexopoulos, Dimitrios 10 Jun '16

10 Jun '16

Hi, We'd like to process pediatric data through the complete FS 5.3 pipeline. The T1/T2 data are acquired with a 3T Siemens as follows: T1 mpr sag - 0.82x0.82x0.85 T2 Space - 1x1x1 We'd like to process using both the T1 and T2 (for better dura removal and possible myelin analysis). Is it possible to use the hires T1 and have data not downsampled to 1x1x1? Ifpossible, can this be done in tandem with the lower resolution T2-space? What recon-all command would be best for this process? 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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