Freesurfer September 2019

freesurfer@nmr.mgh.harvard.edu

93 participants
143 discussions

mri_glmfit: don't display "positive"
by Rockers, Elijah D. 23 Sep '19

23 Sep '19

External Email - Use Caution Hello, with Qdec, there was an option to "remove" positive (or negative) results from the displayed overlay... Is it possible to do something similar with the results of mri_glmfit, but displaying with freeview instead? For instance, if I wanted to exclude regions that appear to have increased cortical thickness when compared to healthy controls? Thanks, Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 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.

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Keep manual edits of older freesurfer versions?
by Joëlle Ismay Rosanne Van Der Molen 23 Sep '19

23 Sep '19

External Email - Use Caution Dear FreeSurfer experts, I have a question regarding manual edits and change of FreeSurfer version. In our lab, we have thus far processed most of our T1 scans using FS version 5.1 and have performed manual edits when needed. We are now updating our processing to FS version 6.0, and would like to use previously edited data (from the 5.1 version) as an input for the FS version 6.0 processing (based on previous emails from the mail archive, I understand this makes sense?). Ideally, I'd like to store the FS6 outputs in a new parent directory (different from the directory where the FS5.1 processing outputs are stored). However, simply running: recon-all -s subject_name -sd /path/to/FS6_outputs/ -all ... with /path/to/FS5.1_outputs/ as a SUBJECTS_DIR doesn't work (it looks for input data in the -sd specified output directory, which doesn't contain anything yet). Adding an -i flag with a full path to the desired output directory also doesn't work: recon-all -s subject_name_FS6 -sd /path/to/FS6_outputs/ -i /path/to/FS5.1_outputs/subject_name/ ... as it says the -i flag needs a file as an input, not a folder. Now, adding an -i flag and giving for instance the 001.mgz as input works: recon-all -s subject_name_FS6 -sd /path/to/FS6_outputs/ -i /path/to/FS5.1_outputs/subject_name/mri/001.mgz However, if I am not mistaken, the manual edits are not stored in this 001.mgz file. Thus, does this mean that when rerunning a new version of freesurfer on already processed data, the same subject folder has to be used as input (FS 5.1 processed data) and output (FS 6 processing outputs)? And if so, should old files (that remain non-modified after the FS6 run) be removed? Thank you in advance for your answer, Best regards, Joëlle van der Molen

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GLM analysis question
by Ferraro, Pilar 23 Sep '19

23 Sep '19

External Email - Use Caution To the kind attention of the FreeSurfer team, I have some questions concerning a GLM analysis I’m running and any help would be greatly appreciated! I’m interested in identifying cortical regions where older age is associated with greater atrophy. However, unlike the example reported in the tutorial page, I do not have two groups (male and females) but just one group (patients, regardless of their gender). - Firstly, I’ve generated an “age.fsgd" file with the following structure: Class Main Variables Age Input subj 1 Main 61 Input subj 2 Main 73 …. And so on. - Secondly, I’ve assembled the data using the mris_preproc command (including resampling, concatenating and smoothing). - Thirdly, I’ve proceeded with the glm analysis using the mri_glm command. However, here I’ve changed the fsgd option, and in particular: —fsgd age.fsgd doss (I thought the DOSS design was more appropriate in my case). FIRST QUESTION: is this correct? Then, I’ve set the contrast in the "lh-Avg-thickness-age-Cor.mtx” file as: 0 1. SECOND QUESTION: is this correct? In this case I’ve set the intercept value as 0 and the slope value as 1. Many thanks for your help, Pilar

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talairach.m3z not found
by Dev vasu 23 Sep '19

23 Sep '19

External Email - Use Caution Dear all, When i run recon-all , i am encountering an error transforms/ talairach.m3z not found during registration phase, could some one please let me know how to resolve this?. Thanks Vasudev

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Fwd: Talairach Failure Dection error for recon-all
by Hang Zeng 23 Sep '19

23 Sep '19

External Email - Use Caution mT1.nii <https://drive.google.com/file/d/1ABR_hATWJP7QisH3TIw1_yZjVaxaucgn/view?usp=…> Dear Freesurfer users, I am trying to run the recon-all command for a T1 imge. The image is bias corrected using spm-segmentation (see attached). And the Talarich Failure Dection error occurred (see the log file). I ran the same analysis with the non-processed T1 and it worked. Any information would be appreciated Best, -- Hang ZENG Institute of Neuroscience and Medicine (INM-3) Forschungszentrum Juelich, Leo-Brandt-Str. 5 52425 Juelich Email: h.zeng(a)fz-juelich.de <zenghang14(a)gmail.com> & zenghang14(a)gmail.com Telefon: +49 2461/61-85328

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freeview command line options
by Rockers, Elijah D. 23 Sep '19

23 Sep '19

External Email - Use Caution Hello, it's possible I found a bug in freeview: I'm using the overlay_color option with freeview. Specifically I am trying to use both the "truncate" and "inverse" options in a command line call to freeview for a pipeline I am building. The documentation says that I can apply more than one, delimited by commas .... however I have found that if I attempt to use both truncate and inverse, it seems to be only applying whichever one appears last on the list. In an interactive instance of freeview, doing everything manually, I have no problems. Just seems to be an issue with the command line call. Any suggestions on how I might proceed in this case? -Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 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.

3 3

Hippocampal Subfields Atlas
by ZZY 23 Sep '19

23 Sep '19

External Email - Use Caution Dear Freesurfer developer:               I have a group of multimode MRI data, including functional MRI, T1WI and diffusion MRI. We want to analyze the functional and structual connectivity between the hippocampal subregions. Now, we have obtained individual-level atlas of hippocampal subfields for each subject by using FREESURFER 6.0 on the T1 image. What should we do next step? How do get a group-level atlas of hippocampal subfields and apply it to functuional and diffusion data? Best, zhiyong

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Default GCA atlas FreeSurfer 6?
by Brehler, Michael 20 Sep '19

20 Sep '19

External Email - Use Caution Hello FreeSurfer experts, can someone tell me what the default GCA atlas for recon-all in FreeSurfer 6 is and where I can find the image? Regards, Michael

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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/>*

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mgz to nifty {Disarmed}
by 郑凤莲 20 Sep '19

20 Sep '19

External Email - Use Caution Hi experts, I am using FS for some studies. Now, I have a question about format convertion. How can I convert .mgz file to .nii file. Is there any way to complete? Thanks for your contention in advance. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

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Freesurfer September 2019