Freesurfer February 2018

freesurfer@nmr.mgh.harvard.edu

119 participants
170 discussions

funcroi-table-sess: how to specify frames for multi-band data
by Keishi NOMURA 03 Feb '18

03 Feb '18

Hi all, I’m using : freesurfer-Darwin-lion-stable-pub-v5.3.0 I’d like to plot HRF for each condition for each subject, using data acquired by multi-band EPI. Here are the commands I used: funcroi-config -roi rh.V1.roicfg -label rh.V1.label -analysis RH_fwhm8 -force funcroi-sess -s ORI01 -roi rh.V1.roicfg -df sessdirfile # m: frames foreach m ( 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 ) funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$m.txt -frame $m end Then I got an error like “Error: input frame = 2, input volume only has 1 frames”. I referred to the related questions: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15883.html https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017958.ht… It seems that there is nothing wrong with these commands, except for specifying the frames. One possibility is that using multi-band data is somehow causing trouble. I’m now using multi-band factor = 8 and TR = 0.8 sec, so then I set the frames to multiple number of TR = 0.8, and ran the commands again: foreach m ( 0.8 1.6 2.4 3.2 4.0 4.8 5.6 6.4 7.2 8.0 8.8 9.6 10.4 11.2 12.0 12.8 13.6 14.4 15.2 16 ) funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$m.txt -frame $m end But still I get errors like “Error: input frame = 2, input volume only has 1 frames”. (when I used frame = 2.4. Hence, it seems that we cannot use non-integral inputs) So, my question is: (1) How should I specify frames when I use multi-band data? (2) Regarding (1), what temporal resolution do I get when I use TR = 0.8? (for example, TER = 0.8/20 = 0.04 or anything like that) (3) Or, is there anything wrong with my commands other than frames? Thank you, Keishi

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How to extract stats of the regions that is covered by large clusters
by Shatil, Anwar Shahadat 03 Feb '18

03 Feb '18

Hello Experts: After running mri_glmfit sim, I got below clusters: ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 16.567 56197 13752.71 -36.8 -15.5 55.0 0.00020 0.00000 0.00040 30900 180209.80 precentral 2 9.630 57862 3018.98 -29.7 -72.0 -10.1 0.00020 0.00000 0.00040 4620 23119.05 fusiform 3 9.488 162470 2465.82 -16.0 -79.3 7.4 0.00020 0.00000 0.00040 4108 19097.47 pericalcarine 4 8.845 35506 1860.62 -24.5 -79.0 23.1 0.00020 0.00000 0.00040 3375 15122.28 superiorparietal 5 6.223 84246 1019.33 -4.8 15.4 -6.3 0.00020 0.00000 0.00040 1760 6950.26 rostralanteriorcingulate However, Cluster-1 area is large compared to others and it actually postcentral, and some portion of paracentral region. How can I extract the stats for these regions? Thanks, Anwar ------------------------------------------------ Anwar S. Shatil Research Assistant, Medical Imaging Sunnybrook Health Sciences Centre Toronto, ON, M4N 3M5 Email: anwar.shatil(a)sunnybrook.ca<mailto:anwar.shatil@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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Spatial smoothing during preprocessing
by Ben Smith 03 Feb '18

03 Feb '18

Hi all, I read from the freesurfer discussion archives that when combining FSL FEAT with freesurfer, one should definitely NOT do spatial smoothing in the preprocessing when preparing to examine cortical data. https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11536.html However I can see that in the FSFast pipeline, 2D and 3D smoothing **is** included in the FSFast preprocessing. So: 1. I am guessing that the 2D smoothing applies only to the surface and is smoothing on the surface space. Is this correct? 2. I'm also guessing that the 3D smoothing applies only to the subcortical regions. Is all this also correct? 3. The freesurfer.feat.ppt guide does NOT contain any instructions for doing any smoothing on data derived from FSL. But I assume that, if smoothing is done during FSFast preprocessing but is not done when preprocessing in FSL, then smoothing will still need to be done at a subsequent point with the FSL data. But I don't see instructions on that in the Freesurfer FEAT documentation on freesurfer.feat.ppt. If I do FSL preprocessing+1st-level analysis with no spatial smoothing, and then proceed with the analysis, at which point do I apply preprocessing? Is there a guide specifically describing how to apply smoothing to data originating from FSL? Thank you very much to anyone willing to help! Best regards Ben _______________________ Ben Smith, MSc. Ph.D. Candidate University of Southern California https://bjsmith.github.io/ w | +1 213-740 7851 m | +1 323-385 9349 skype | ben.smith.nz

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Problems transforming T1 to talairach
by Helen Beaumont 03 Feb '18

03 Feb '18

I am using the command mri_convert -at transforms/talairach.xfm brain.mgz brain_in_tal.nii.gz to convert a native-space skull-stripped T1 image to talairach space. I used recon-all to generate the transform matrix, and the segmentation and everything look good. But the T1_in_talairach image is not good - the brains are ending up different sizes, and frequently have the posterior chopped off. Please what am I doing wrong? Should I be applying the inverse of the transform? Helen Beaumont PhD University of Manchester

2 1

Group and ROI analyses in qdec
by Backhausen, Lea 03 Feb '18

03 Feb '18

Dear freesurfer experts, I started using qdec for comparing cortical measures in adolescent patients with ADHD versus typically developing adolescents and I have a few questions concerning the ROI analysis as well as the Desikan-Killiany versus Destrieux atlas. English is not my native language so please excuse typing errors or wrong expressions. 1) Is it somehow possible to have the significant clusters mapped onto the Destrieux atlas in qdec instead of the Desikan-Killiany one? 2) I would like to export the mean thickness/surface area from significant clusters to SPSS to correlate them with clinical symptoms. I understand you can either use means from the stats tables (aparc_thikness_lh.txt etc.) or manually draw a ROI and then map the lable back to other subjects. But is there also a way to simply export the measures from the significant clusters that show up without drawing around them or export measures from the peak vertices? 3) If I use methods as described in 2), do I have to be concerned about ‘double dipping’ or ‘circular analysis’? 4) Does the measure ‘area.pial’ you can select during design creation correspond to ‘cortical surface area’ and the measure ‘area’ to ‘WM surface area’? Which measure do the aparc_area_lh.txt files that I get when generating stats data tables correspond to? I do not see aparc_area.pial.txt files, should I be getting them? 5) After reading a lot about correcting for global brain measures I am still confused about the best way to do it. I am quite sure that for the volume-based measures it is best to control for ICV/eTIV but for thickness and surface area I read different approaches from not controling to using total brain volume, global thickness or ICV. Is it safe not to control for anything for thickness measures as I do not expect any kind of atrophy in my sample? What should my decision be based on? Sorry, these are many questions – I appreciate any thoughts on these problems, thank you so much! Lea Backhausen, B.Sc. Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the Technische Universität Dresden, Dresden, Germany

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White matter hypointensities
by Maksimovskiy, Arkadiy 03 Feb '18

03 Feb '18

Dear Experts, I was wondering if anyone might know why the WM hypointensities total number in aseg does not match the sum of left and right white matter hypointensities. Thanks, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

2 1

talaraich transformation error
by Dijkshoorn, A.B.C. (Aicha) 03 Feb '18

03 Feb '18

Hello free surfer developers, I am attempting to compute cortical thickness for anatomical ROIs in neonates, but for some of my subjects I get the following error when I run the auto-recon1 command: \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin leia.ds.umcutrecht.nl 14.5.0 Darwin Kernel Version 14.5.0: Sun Jun 4 21:40:08 PDT 2017; root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64 recon-all -s N192_con_recon exited with ERRORS at Fri Feb 2 12:32:02 CET 2018 Is there any way I can work around this error? Kind regards, Aicha Dijkshoorn

2 1

Re: [Freesurfer] annotation to volume with custom color scheme (Yeo parcellations)
by Dorit Kliemann 02 Feb '18

02 Feb '18

ops. I guess that should have been obvious to me! Thanks! Dorit

1 0

segmentHA_T2.sh
by Eva Hilland 02 Feb '18

02 Feb '18

Dear freesurfer experts, I have tried the dev version of Segmentation of hippocampal subfields and nuclei of the amygdala for OSX el Capitan, downloaded today. I did get an error message similar to a previous error I found on this mailing list: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054973… I have pasted the hippocampal-subfields-T2.HippoAMYT1andT2.log below Is this a matlab runtime problem? Many thanks in advance Eva -------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) left Wed Jan 31 22:36:38 CET 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64: Invalid MEX-file '/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64': dlopen(/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv Referenced from: /tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 (which was built for Mac OS X 10.11) Expected in: /usr/lib/libstdc++.6.dylib in /tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 Error in kvlClear (line 11) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 135) MATLAB:invalidMEXFile Darwin Evas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 T2 hippocampal subfields exited with ERRORS at Wed Jan 31 22:36:49 CET 2018

3 2

Control Points Not Working
by Arsenije Subotic 02 Feb '18

02 Feb '18

Dear experts, I’m currently performing quality control for my data, and most of my issues so far have been that in many cases adding control points has not been able to extend the white surface. I’ve also noticed that most of the regions where I have needed to add CPs are in the parietal regions of the brain. Does anyone know how many control points are usually recommended to be added? I have so far had cases where I have had to add hundreds of CPs and I have still had mixed success. Thank you, Arsenije

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Freesurfer February 2018