Freesurfer April 2019

freesurfer@nmr.mgh.harvard.edu

99 participants
136 discussions

Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

4 4

Correct for sulcuses & ventricles size
by John Anderson 13 Dec '20

13 Dec '20

External Email - Use Caution Dear Freesurfer experts, I have two groups of subjects (healthy and patients). The patients have different degrees of atrophy. Looking into the individual scans, the subjects are largely different in the space between the sulcuses and the size of ventricles. My questions are: 1. Is there any way to correct for these differences in the surface based analysis? 2. Including eTIV covariate does it help in this case? 3. Does the resampling to "fsaverage" overcome the challenge of these differences between the subjects? I appreciate any advice, John

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Error with "recon-all -make all" following multiple manual editing
by Matthieu VANHOUTTE 03 Jul '20

03 Jul '20

External Email - Use Caution Dear Freesurfer's experts, Havng done multiple types of manual editing in two subjects, I relaunched the recon-all process (Freesurfer 6.0.1) with the flag "-make all". However, during the process, I goth for both subjects the following error message: / / /make: *** [/netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv1s097/mri/aseg.presurf.mgz] Error 1/ /recon-all -s /netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv3s024 -ccseg ERROR: Flag -ccseg unrecognized./ Following the troubleshooting site (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0) I have over-writed the "recon-all.makefile" file since I use the 6.0.1 version of Freesurfer. Thanks for helping. Best, Matthieu

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group analysis of large data sets
by Wang, Xin 22 Apr '20

22 Apr '20

Hello, FreeSurfer Group, What is the maximal matrix size for glm_fit process? How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes? Thank you. Xin

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eTIV vs. ICV
by Alexopoulos, Dimitrios 20 Apr '20

20 Apr '20

External Email - Use Caution The eTIV from FS 6.0 has been used by many as a normalization measure for regional volumetric analyses. I know it is not a true voxel count but does it conceptually include extra-axial CSF or is it more a total tissue volume? Jim ________________________________ 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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Highlighting single atlas structures in freeview
by Francesco Puccettone 05 Feb '20

05 Feb '20

External Email - Use Caution Dear all, I would like to show several structures from the DKT (or the Desikan-Killiany) atlas alone on a "blank" fsaverage brain, rather than have all structures displayed in different colors (as happens by default). For instance, I'd like to just show "medialorbitofrontal" on its own, then "middletemporal" on its own, etc. After I open the parcellation, freeview -v /FS/fsaverage/mri/aparc+aseg.mgz:colormap=lut:opacity=0.4 -f /FS/fsaverage/surf/lh.white:annot=aparc.annot , I expected to be able to turn each label in the list on and off like a layer, but this does not work. [image: 21-01-2019 14.48.54.jpg] I hoped I could use Alt+F to hide/show each atlas label at a time (cf freeview tutorial <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview>), but this instead toggles the entire external surface of the brain on and off. Can anyone help? Thank you! --Francesco

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Course in Advanced Neuroimaging (Barcelona)
by Erick Canales 20 Sep '19

20 Sep '19

Dear colleagues, I am pleased to announce our upcoming Course in Advanced Neuroimaging held annually in Barcelona. It takes a practical approach and does not require qualifications or previous experience in neuroimaging. It will be taught in Spanish. The multidisciplinary programme provides thorough training in the analysis of brain images from different MRI modalities and data modeling techniques, including voxel-based morphometry, cortical thickness, diffusion tensor imaging, fibre tracking, functional MRI and brain connectivity, as well as the statistical methods behind these techniques including elements of meta-analysis, and more. The course consists of a five-month online theoretical module (starting on November 6th) and a period of practical face-to-face training (split between two days in November and two weeks at the end of April) held in Barcelona. For further information, please visit the website: www.cursoneuroimagen.com Best regards, Erick J. Canales-Rodríguez Joaquim Radua Raymond Salvador Edith Pomarol-Clotet FIDMAG Research Foundation and Sociedad Española de Neuroimagen *www.fidmag.com <http://www.fidmag.com/>*

1 1

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

2 12

T2 seq. for hippocampus ??
by Anik Dar 25 Jun '19

25 Jun '19

External Email - Use Caution Hi All, I have 1x1x3 cubic mm T2 and 1x1x1 cubic mm FLAIR, in addition to 1x1x1 cubic mm MPRAGE. Can you please let me know whether I should use only T1 or should I use one of the additional seq. for hippocampal subfield segmentation ? cheers Nik

3 4

MP-RAGE protocol
by mustafa amin 20 May '19

20 May '19

External Email - Use Caution Dear Freesurfer experts, I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance. Yours faithfully, Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara

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Freesurfer April 2019