Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

T2 flair as additional scan in hippocampal subfields segmentation
by Rovai Antonin 30 Aug '19

30 Aug '19

External Email - Use Caution Hello I’d like to know if there is any advantage in having a T2 FLAIR as additional scan (in addition to our 1mm isotropic T1 scans) when using the hippocampal subfield segmentation tool. We do not have T2 nor PD available. Thanks for you help Antonin Rovai Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

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viewport does not affect snapshots for --slice option in cmd mode
by Hoke, Harris 29 Aug '19

29 Aug '19

Freeview does not update in the viewer window to the correct slice position when calling on viewport. This means instead of taking snapshots of N slices of the brain from N specified slice coordinates, it takes the same snapshot over and over again. Originally, we found a workaround by disabling qt_setup in the freeview tcsh script: #source $FREESURFER_HOME/bin/qt_setup. After this, it worked perfectly. Since then, it has stopped working well. The error occurs for saggital and coronal views. (Axial works fine, for some reason). I am using the stable release of freesurfer 6.0.0. The problem still happens if I interleave axial/coronal/saggital viewport commands, instead of running them together as below. The problem also occurs using the development version of freesurfer from august 27th, CentOS7 build (but only for sagittal and coronal; Axial works fine). freeview -cmd minimalcmd.txt minimalcmd.txt: freeview -v SUBDIR/mri/orig/001.mgz -layout 1 -cc -nocursor -viewport sagittal -slice 80 127 127 -ss OUTDIR/T1_sag_1.jpg -noquit -viewport sagittal -slice 90 127 127 -ss OUTDIR/T1_sag_2.jpg -noquit -viewport axial -slice 127 80 127 -ss OUTDIR/T1_ax_1.jpg -noquit -viewport axial -slice 127 90 127 -ss OUTDIR/T1_ax_2.jpg -noquit -viewport coronal -slice 127 127 80 -ss OUTDIR/T1_cor_1.jpg -noquit -viewport coronal -slice 127 127 90 -ss OUTDIR/T1_cor_2.jpg -noquit -quit In case it's useful: uname -a Linux ncfservice02 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux I'm unsure what else I can try or what other information I can provide. Please let me know.

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how to get the displacement from template to the linearly registered image
by ping cao 29 Aug '19

29 Aug '19

External Email - Use Caution Dear expert， I saw a paper mentioned this ： By using the *deformation field* from nonlinear registration, we can > build the correspondence between voxels in the template and each > linearly-aligned image. For instance, for each voxel (x, y, z) in the > template image, we can find its corresponding voxel (x + dx, y + dy, z + > dz) in each linearly-aligned image, where (dx, dy, dz) is the > *displacement* from the template image to the linearly-aligned image > defined by the deformation field. So, I want to get the deformation field from the template to the linearly registered image(flirt_T1). Can Freesurfer do this? Which file is a linearly registered image that does not contain an affine transformation? How can I get this deformation field? Your help is greatly appreciated. Best, ping

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New fsaverage
by Westeneng, H.J. 29 Aug '19

29 Aug '19

External Email - Use Caution Dear FreeSurfer experts, It has previously been reported that vertex 40969 is the same as vertex 0, which creates a very large triangle in fsaverage (appearing as a defect in freeview) and is fixed in the development version. For our research we would very much appreciate to use the new fixed version of fsaverage. In the release notes (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) it has been mentioned that a post to this list is needed to get the new fsaverage version. I hope anyone can help me to get this new version. Kind regards, Henk-Jan ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Invalid Key Error for Freesurfer 5.1
by An Lijun 29 Aug '19

29 Aug '19

External Email - Use Caution Dear Freesurfer experts, Right now I am trying to use Freesurfer 5.1.0. But the software showed ERROR “Invalid FreeSurfer license key found in license file”. We tried to apply license online, however, the license provided online is now for 6.0.0 version and it seems not applicable for 5.1.0 since I still got the same error message as before. May I ask how to get the licnese of 5.1.0? The tricky part is the format of lecense now I get from Fresssurfer is different from the old one in Freesurfer 5.1. New License I get(call license.txt): xxxxxxxx(a)gmail.com<mailto:xxxxxxxx@gmail.com> 43508 *CRBDdLNbgmws FSOkaDD5AxOQk Old License(call .license): xxxxxxxx(a)gmail.com<mailto:xxxxxxxx@gmail.com> 39689 *1 PS: I tried to use `dos2unix` to transfer the license to unix format, but it seems no help. Thanks for your help! ------------------------------------------------------------------------------------------------------------------------------------------ Best Regards, An Lijun

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Time course thalamic subregions
by stdp82＠virgilio.it 28 Aug '19

28 Aug '19

External Email - Use Caution Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS. I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223 The command produces this error: ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 169 105 118 Please, I have other questions for you. 1) At starting, I have used the command line reported below: preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd The -mni305-1mm could be more useful? My raw-data are: data_type UINT16 dim1 64 dim2 64 dim3 48 dim4 140 datatype 512 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ 2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? 3) If I interested to obtained the time course from a unique region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added? Thanks, Stefano

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An error during data processing
by Троицкий Антон Александрович 28 Aug '19

28 Aug '19

External Email - Use Caution Hello FreeSurfer Developers, I a beginner freesurfer user. It is my first patient that I try to process. The patient data was obtained on Philips MRI Achieva 3.0 T with dStream application. I performed /Applications/freesurfer/bin/recon-all -i /Users/anton.troitskii/Documents/FreeSurferData/Patients_input/2018-08-19/DICOM/IM_0001.dcm -subject Test1 -all The process started and an error occurred. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0 2) Platform: macOS Sierra 10.12.6 3) uname -a: Darwin mac-2ap023-2.fccho-moscow.ru<http://mac-2ap023-2.fccho-moscow.ru> 16.7.0 Darwin Kernel Version 16.7.0: Thu Jan 11 22:59:40 PST 2018; root:xnu-3789.73.8~1/RELEASE_X86_64 x86_64 4) recon-all.log: see attached Best regards, Anton Troitskii.

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ERROR reading /<my data path>/fsaverage/label/lh.BA1_exvivo.label with recon-all.log
by liuxingze1993 28 Aug '19

28 Aug '19

External Email - Use Caution Hello，Dear FreeSurfer Developers, I’m a doctoral student from Xiangya 2nd Hospital of Central South University, and also a beginner to FreeSurfer. I'm attempting to follow the steps descripted on ‘Practice Working with Data’ (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice) with our own data, but I’ve met the same problem several times when I programing the command ‘recon-all -all -i 61492283 -s Sub219’: (**ps: 61492283 is the T1 file I found after programing the command 'dcmunpack -src . -scanonly.log') SUBJECTS_DIR /media/dell/AA32E/Data_prac/219/20181211/19470000 (**PS: 19470000 is the folder where the T1 located) FREESURFER_HOME /usr/local/freesurfer Loading source label Invalid argument ERROR reading /media/dell/AA32E/Data_prac/219/20181211/19470000/fsaverage/label/lh.BA1_exvivo.label recon-all -s Sub219 exited with ERRORS at <local time here> I've searched the ‘lh.BA1_exvivo.label’ file in the related path and no such file here. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu14.04 LTS 3) uname -a: Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank u for viewing, and I will be waiting here for your professional advice !

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Converting a binary overlay file to label
by Nillo, Ryan Michael R 28 Aug '19

28 Aug '19

External Email - Use Caution Hello FreeSurfer users/developers. I manually created a binary overlay file on the pial surface. I am interested in looking at regions outside of this overlay file, so I converted lh.cortex.label to a binary overlay file and took the difference between the two. I want to take this new file and create a label so that I can run mris_anatomical_stats on the new region. How might I do this? Sent from my iPhone

2 1

Segmentation fail
by Giovana dos Santos Cover 28 Aug '19

28 Aug '19

External Email - Use Caution Dear Freesurfer experts, I am trying to segment the white and pial matter from my MR images but for some reason, the final segmentation always misses some brain areas. I attached here a nu and brainmask image with the segmentation as an example. The MR image I am using is a MEMPRAGE 0.5mm resolution acquisition from a 3T Siemens TrioTim scanner, possibly with a 64 coil channel. Can you please help me figure out how I could improve the segmentation? I am using the following command: recon-all -autorecon1 -autorecon2 -autorecon3 -s hires_test -hires -i high_res.nii On another note, the full recon-all command takes around four days to finish in an 8GB ram mem computer. I would appreciate if you happen to have any suggestions on how I could run it faster, if this is even possible. Thanks Gio.

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