Freesurfer September 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
160 discussions

A Question about Estimating the Cortical Thickness for Each Subregion
by Maedeh Khalilian 06 Sep '18

06 Sep '18

External Email - Use Caution Dear Freesurfer Experts; I have a question, are there any ways in FreeSurfer to estimate the gray matter volume or cortical thickness of each region after parcellation, in order to define the edges in the brain network? Kind regards, Maedeh,

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how to dilate a mgh binary mask file in fsaverage space. The file is in .mgh format.
by Anik Dar 05 Sep '18

05 Sep '18

External Email - Use Caution Hi I have created a .mgh file which is a bunch of vertices all with a value of 1. Please see pic. [image: Screen Shot 2018-09-05 at 7.06.04 PM.png] I want to create a bigger region of interest by dilating this yellow region lets say with a radius of 10 vertices around this region. How to do it ? Thank you. Ani

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Resting-State and Brain Connectivity 2018: Early registration fee applies until September 14, 2018
by Kelvin Mok 05 Sep '18

05 Sep '18

External Email - Use Caution ---------- Forwarded message --------- *From:* Amir Shmuel, Dr. *Subject:* Resting-State and Brain Connectivity 2018: Early registration fee applies until September 14, 2018 *Resting-State and Brain Connectivity 2018: *Early registration fee applies until September 14, 2018 Educational course: September 24-25 Conference, featuring 45 world-renowned speakers: September 26-28 Satellite workshop on how to incorporate machine and deep learning in your data analysis: September 29 *http://restingstate.com/2018/ <http://restingstate.com/2018/>* *Amir Shmuel* *Chair of the organizing committee* *Resting-State and Brain Connectivity 2018* *Montreal, QC, Canada* *[image: http://restingstate.com/2018/wp-content/uploads/2017/06/resting-state-logo-…

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Mean FA values for major tracts all greater than 1
by Katherine Damme 05 Sep '18

05 Sep '18

External Email - Use Caution Hello Freesurfer Support group, I have run tracula on hundreds of subjects for a study and their primary tracts are all showing that MFA is greater than 1. Typically, I expected that MFA should be in the .3 to 1 range. Should I be suspicious that these MFA values are over the top of that range or is this common for major tracts like the forceps major? Thank you for your insights on this potential error. Kate

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mris_compute_parc_overlap average minimum distance measurement
by Zimmerman, Jared 05 Sep '18

05 Sep '18

External Email - Use Caution Hi Freesurfers, I’m using mris_compute_parc_overlap to compare the similarity between two parcellations and I’m curious about how the average minimum distance measurement is calculated. The help text for the function says “… a table of mean minimum distances between corresponding labels.” My questions are 1) what set of measurements is being meaned here, and 2) what exactly is the measurement. My current interpretation is that for every vertex in annot1 the minimum distance to a vertex in annot2 with the same label is calculated such that overlapping regions have a distance of zero. The mean is then calculated over these distance measures for all vertices in a given label. If this is true, do you recommend doing any subject level corrections? Seems like subjects with larger cortical surface areas would be biased to have larger distances. Thanks, Jared

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long_mris_slopes: error: cannot create a table with longitudinal pc1
by Shatil, Anwar Shahadat 05 Sep '18

05 Sep '18

External Email - Use Caution ?Dear Doug: I am trying to get a table containing pc1 values for each subject in a longitudinal study and failed to extract this. I use the code below: long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-pc1.dat It says long_mris_slopes: error: no such option: --out-pc1 However in the --help file it says: Within-Subject Output: Pass these to overwrite the default names: --out-avg=OUT_AVG filename to store temporal average in <template>/stats/<OUT_AVG> (default: long.<stats>.<meas>-avg.dat) --out-rate=OUT_RATE filename to store rate in <template>/stats/<OUT_RATE> (default: long.<stats>.<meas>-rate.dat) --out-pc1fit=OUT_PC1FIT filename to store pct. change (to tp1fit) in <template>/stats/<OUT_PC1FIT> (default: long.<stats>.<meas>-pc1fit.dat) --out-pc1=OUT_PC1 filename to store pct. change (to tp1) in <template>/stats/<OUT_PC1> (default: long.<stats>.<meas>-pc1.dat) --out-spc=OUT_SPC filename to store sym. pct. change in <template>/stats/<OUT_SPC> (default: long.<stats>.<meas>-spc.dat) --out-resid=OUT_RESID filename to store residual in <template>/stats/<OUT_RESID> (default: long.<stats>.<meas>-resid<resid>.dat), requires --resid <int> --out-stack=OUT_STACK filename to store stacked measure file <template>/stats/<OUT_STACK> (default: long.<stats>.<meas>-stack.dat) Stacked Tables: To output tables with results from all subjects --stack-avg=STACK_AVG full filename to stack temporal average tables (default no stacking) --stack-rate=STACK_RATE full filename to stack rate tables (default no stacking) --stack-pc1fit=STACK_PC1FIT full filename to stack pct. change to tp1fit tables (default no stacking) --stack-pc1=STACK_PC1 full filename to stack pct. change to tp1 tables (default no stacking) --stack-spc=STACK_SPC full filename to stack sym. pct. tables (default no stacking) --stack-resid=STACK_RESID full filename to stack residual tables (default no stacking)? Am I writing the code wrong?? I never got any long.<stats>.<meas>-pc1.dat file in <template>/stats/ folder except bunch of mgh files in <template>/surf/ folder. Thanks, Anwar -- Anwar S. Shatil Research Assistant Department of Medical Imaging Sunnybrook Health Sciences Centre Room AB204, 2075 Bayview Avenue Toronto, ON M4N 3M5 Tel: 416.480.6100 ext. 89617 Email: anwar.shatil(a)sunnybrook.ca This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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Get corresponding vertex of another subject
by Michael . 05 Sep '18

05 Sep '18

External Email - Use Caution Hi, i want to create a lookup table for the vertex correspondence between the subjects A & B (pial files). e.g verticesA(100) corresponds to verticesB(122) Of course the number of vertices is different between the subjects, e.g one vertex of A can correspond to several vertices from B. Currently, I am reading in the pial files of subject A using 'read_surf' and create two label files (lh/rh) containing all vertices. In order to get the corresponding vertices of Subject B, i use "label2label". label file A: #!ascii label, from subject 142350 0 -7.814680 -88.725967 9.598738 1.000000 1 -8.505306 -88.835274 9.457685 2.000000 2 -9.234029 -89.900490 9.420641 3.000000 resulting label file: #!ascii label , from subject cvs_avg35_inMNI152/Segmentation vox2ras=TkReg 137427 888 -7.179 -84.047 -28.333 1.0000000000 642 -7.533 -84.272 -28.382 2.0000000000 637 -7.717 -84.612 -28.118 3.0000000000 But how can I interpret the result? Can I assume that verticesA(0) corresponds to verticesB(888)? Or verticesA(0) corresponds to verticesB(888)? Or is there another way to create such a lookup table? Thank you in advance!

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Is voxel size resampled during recon-all? And different voxel size in longitudinal studies
by Daniel Ferreira 05 Sep '18

05 Sep '18

External Email - Use Caution Dear colleagues, I was wondering if resampling voxel size is done during recon-all. Also, I have data with voxel resolution of 1x1x1 mm at baseline and 1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation by default (or can be performed by any way) that minimizes these differences in somehow. Thank you very much Dani -- *Daniel Ferreira, PhD, Assistant Professor* Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences and Society Karolinska Institutet (Sweden) *Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: daniel.ferreira.padilla(a)ki.se <daniel.ferreira.padilla(a)ki.se>*

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error in selxavg3-sess - mismatch TE
by stdp82＠virgilio.it 05 Sep '18

05 Sep '18

External Email - Use Caution Hi list, I have run the FS-FAST analysis in line with the standard procedures that I use routinely. With new data, selxavg3-sess produces an errror: there is a mis-matched between the TE in the analysis (=3) and the TE in the data (=0). I have cheched the data information by fslinfo as well as MELODIC and both the operations confirm the data have a TE=3 that matches with TE reported in mkanalysis-sess . How is it possible? Please, could you help me? Thanks Stefano

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SurfaceRAS to Vertex coordinate system
by Bruss, Joel E 04 Sep '18

04 Sep '18

External Email - Use Caution If I load, say, orig.mgz and lh.pial, in FreeView and lay my cursor on a point, I can see RAS (and surfaceRAS) as well as TKReg RAS (orig) coordinates. Following the steps laid out on the CoordinateSystems web page I can convert back and forth between those coordinate systems. However, I can't figure out what I need to do to calculate the Vertex coordinates. I can load lh.pial in matlab and see the (+1) vertex number and coordinates, but I'd like to figure out the best way to get from Vertex x/y/z to TkReg RAS or SurfaceRAS. Is there an easy formula to calculate this? Thanks in advance for any and all responses. -Joel ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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Freesurfer September 2018