Freesurfer January 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
132 discussions

ROI Correlations
by Swanson,Clayton 26 Jan '21

26 Jan '21

External Email - Use Caution Hi Freesurfer Folks, I am wondering if it is possible to perform an ROI correlation which can then be viewed on the brain similar to whole brain GLM analysis in Freeview. If so, how would I go about performing this type of operation as to specify that particular region. I have two groups (HC and MS) and would like to see if there is an association between paracentral gyrus thickness and performance of a lower limb motor task. Thanks for any help you can provide, Clayton ________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Candidate Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson(a)colostate.edu<mailto:Clayton.Swanson@colostate.edu> (He/Him)

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question on GLM
by Barletta, Valeria 26 Jan '21

26 Jan '21

Good evening Freesurfers! I am building a GLM with 4 classes (control_F, control_M, patient_F, patient_M) to check for differences in cortical thickness between patients and control accounting for the effect of gender and age on cortical thickness. How should my contrast be? Thanks a lot, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823

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lh.pial and rh.pial ALIAS, become lh.pialT1 and rh.pial T1 in Freeview
by Erika Nolan 26 Jan '21

26 Jan '21

External Email - Use Caution Hello everyone, I am new using FreeSurfer and would really appreciate your help with an issue I am encountering when running recon-all (using: recon-all -subject subjectname -i filename.nii -all and recon-all -s TEST2 -i 103515_t1_final.nii -3T -mprage -hires -all). I am using HCP data. Although my white surface reconstruction seems fine, I am having an issue with the gray matter reconstruction: the rh.pial and lh.pial come out as alias files (see attached screenshot) and when I open them in Freeview they open as rh.pialT1 and lh.pialT1 instead! How do I rectify this situation? Thank you for your help, Erika

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dt_recon error: dimension mismatch between y and X
by Antti Cajanus 26 Jan '21

26 Jan '21

External Email - Use Caution Dear FS experts, I’m attempting to run dt_recon on my own DWI DICOM file with registration to corresponding structural data, as described in FS diffusion tutorial (https://secure-web.cisco.com/1zJ4MwZjBaZucnMqD07gGW81VRhJOuT2j8dl2ILpEXoVY0… <https://secure-web.cisco.com/1zJ4MwZjBaZucnMqD07gGW81VRhJOuT2j8dl2ILpEXoVY0…>) I’m using FS version freesurfer-darwin-macOS-7.1.1-20200811-8b40551 on Mac (MacOS Big Sur v. 11.1). I’ve already succesfully run recon-all on the T1 scan. However, when I’m running the dt_recon, I’m getting the following error: Command I’m using: dt_recon --i $TUTORIAL_DIR/$subj/orig/DTI/S142783/NIFD_1_S_0001_MR_dti_WIP_b2000_64dir__br_raw_20120306104435815_50_S142783_I288323.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon ERROR: dimension mismatch between y and X. y has 65 inputs, X has 66 rows. I’ve searched the archive, however not finding any similar issues. Does anyone have an idea how to solve this error? Attached is the dt_recon.log. Best, Antti Cajanus

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Repost: 3DClustSum / AFNI AlphaSim
by Meike Hettwer 25 Jan '21

25 Jan '21

External Email - Use Caution Dear Freesurfer experts, I ran a glm analysis a while back and corrected for MC using the glm-fit_sim --cache option / Monte Carlo simulation. I now saw that the AlphaSim algorithm this is based on is not recommended anymore (https://secure-web.cisco.com/1gjek7zlcbcYDPExwd6Q8QqFRYe58U8joj8TuDwem7t-l6…) Instead, it suggests using 3DClustSim. 1. Does that mean the Monte Carlo simulation as it is implemented in FreeSurfer does not allow for valid analyses / MC corrections anymore? 2. Is 3DClustSim implemented in Freesurfer? And if not, would I need to export the FreeSurfer files as a volume (i.e. 3D) file and analyse it externally? What would you recommend? (My analysis is a regression analysis for one group, so the design matrix is not really suitable for a permutation). Thanks in advance, Meike

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To Run -lGI without Recon-all
by Na, Xiaoxu 25 Jan '21

25 Jan '21

External Email - Use Caution Dear FreeSurfer Experts, I happened to have a task to run lGI, however this time, I couldn't run from the very beginning to start with recon-all as usual. I have already prepared ?h.pial from outersurf.vtk using mris_convert. Is this correct? May I know how to deal with the problem in red as below and what else to be prepared essentially other than this? I may figure out more if that's simple files to generate. I've gotten ?h.area, ?h.thickness, ?h.volume, segmentation already. Thank you so much! ~/test-G$ recon-all -s subject-1 -localGI Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b Current Stamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b INFO: SUBJECTS_DIR is /home/xiaoxu/test-G Actual FREESURFER_HOME /home/xiaoxu/freesurfer -rw-rw-r-- 1 xiaoxu xiaoxu 31435 Jan 22 14:19 /home/xiaoxu/test-G/subject-1/scripts/recon-all.log Linux xnVMUbuntu18 5.4.0-59-generic #65~18.04.1-Ubuntu SMP Mon Dec 14 15:59:40 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux '/home/xiaoxu/freesurfer/bin/recon-all' -> '/home/xiaoxu/test-G/subject-1/scripts/recon-all.local-copy' ~/test-G/subject-1/mri/transforms ~/test-G/subject-1 ~/test-G/subject-1 #@# pial curv lh Fri Jan 22 15:59:28 CST 2021 cd /home/xiaoxu/test-G/subject-1/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial Update not needed #@# pial area lh Fri Jan 22 15:59:28 CST 2021 cd /home/xiaoxu/test-G/subject-1/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial Update not needed #@# pial curv rh Fri Jan 22 15:59:28 CST 2021 cd /home/xiaoxu/test-G/subject-1/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial Update not needed #@# pial area rh Fri Jan 22 15:59:28 CST 2021 cd /home/xiaoxu/test-G/subject-1/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial Update not needed /home/xiaoxu/test-G/subject-1/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Jan 22 15:59:28 CST 2021 mris_compute_lgi --i lh.pial ================= rm -Rf /home/xiaoxu/test-G/subject-1/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /home/xiaoxu/test-G/subject-1/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /home/xiaoxu/test-G/subject-1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... conforming output volume setting resolution for intermediate calculations to 1.0000 error: volume size must be greater than 0 in every dimension ERROR: mris_fill -c -r 1 lh.pial /home/xiaoxu/test-G/subject-1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz failed! Command exited with non-zero status 1 @#@FSTIME 2021:01:22:15:59:28 mris_compute_lgi N 2 e 0.76 S 0.07 U 0.68 P 100% M 151256 F 0 R 43901 W 0 c 9 w 22 I 0 O 0 L 0.12 0.04 0.06 @#@FSLOADPOST 2021:01:22:15:59:29 mris_compute_lgi N 2 0.19 0.06 0.07 Linux xnVMUbuntu18 5.4.0-59-generic #65~18.04.1-Ubuntu SMP Mon Dec 14 15:59:40 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subject-1 exited with ERRORS at Fri Jan 22 15:59:29 CST 2021 For more details, see the log file /home/xiaoxu/test-G/subject-1/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1IirEH-QHYbP-VlpZ8Ta_sE9bJzBhRQSQC9X6cw8h90JlDp… Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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command terminated by signal 11?
by KennethSPrice 25 Jan '21

25 Jan '21

External Email - Use Caution Hell Freesurfers, When running recon-all on a T1 image, I keep getting the error "Command terminated by signal 11" during mris_fix_topology. After manually editing brainmask.mgz and wm.mgz, I made sure that there were no larger defects and ran recon-all again. Still terminated by signal 11. Next, I tried: recon-all -autorecon2 -autorecon3 -skullstrip -no-wsgcaatlas -s hires -clean-bm :"Command terminated by signal 11". This time mris_fix_topology got through lh and got stuck on rh. Any idea on what to try next? Sent with [ProtonMail](https://secure-web.cisco.com/1WCB0vjqi1v_P1iPxErlGHm1UlxO4F8R6l… Secure Email.

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mri_glmfit-sim
by Nasiriavanaki, Zahra 25 Jan '21

25 Jan '21

Hi Freesurferers I am running mri_glmfit-sim to do multiple comparison correction with the command below. It goes through without any error. However when I view the corrected maps in tksurfer, I see some clusters in corrected map with p=2 and p=3, but I don’t see them in corrected map with p=1.3 (images attached). The contrast of interest is the same between the maps. The viewing threshold is 1.3 in p=1.3 maps and is 2 and 3 in the p=2 and p=3 maps respectively. I’m confused. Could you please comment on that? mri_glmfit-sim --glmdir main.wls --cache 1.3 abs --3spaces mri_glmfit-sim --glmdir main.wls --cache 2 abs —3spaces Thanks a lot Mona [cid:BD49B8CB-5370-4E8C-9AD1-CA3BF1F809EE@hsd1.ma.comcast.net] Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Boston, MA, USA, 02129

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Cannot find rh.white.H
by Andy Worth 25 Jan '21

25 Jan '21

External Email - Use Caution Hello, We're seeing this error a lot: "Cannot find rh.white.H" which is generated here <https://secure-web.cisco.com/1kFmpUflCYrLlkn0X825hErhILvuejPNzV2WrombAVtg_s…>. It does not occur if -parallel is turned off. I see that reconbatchjobs does "exec" on the commands sequentially in the order of the list, but it runs each in the background: exec $JOB >> $LOG 2>&1 & so I thought it might just be slightly possible that these two commands: set cmd1 = (rm -f $hemi.white.$suffix) set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix) could end up in a race condition where the file is linked and then immediately removed if somehow the ln command is executed before the rm command. However, I tried reproducing this behavior with a test script but the rm always happens before the ln. Any help would be appreciated! Thanks, Andy Worth Scientific Solutions Engineer he, him, his <http://secure-web.cisco.com/1KxdUXSlflua-8jA7AL5CzR1vwNWqcPAt_z76LcUsPIdfrR…>

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Cerebellar Segmentation Definitions
by Horn, Mitchell Jacob 25 Jan '21

25 Jan '21

Hi FS Experts, I am planning to use the cerebellar segmentations in the routine recon-all which parcellates the cerebellum into cerebellar-white-matter and cerebellar-gray-matter. I am trying to define the two terms, as it appears that the cerebellar-white-matter label includes much if not all the deep-gray nuclei of the cerebellum (which is ideal, due to resolution and size of these structures). Is there a reference I can specifically point to that details the labels and further the inclusion of these deep grey structures in the cerebellar-white-matter? I could not easily track down the correct FS white paper for this. Thanks in advance, Mitch

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Freesurfer January 2021