Freesurfer June 2022

freesurfer@nmr.mgh.harvard.edu

84 participants
123 discussions

Recon All
by Amar Shukla 21 Jul '22

21 Jul '22

External Email - Use Caution Dear Sir, I am a PhD scholar using the freesurfer tool to conduct my research work. I tested the recon all method in the Free Surfer, and it was effective with the data set that was used by me. What are the exact default parameters for the different processes of recon all that were used in motion correction, intensity normalization, etc?. It would be really helpful if you could provide me with the link or the article where it is explained clearly, this will help me to get through these processes in more depth and in a more constructive manner. Although the Free Surfer website has an FAQ regarding this process, there are no clear explanations about what the default parameters are during recon all. -- With Regards, Amar Shukla PHD Scholar UPES

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recon-all error: mri_cc
by cooperr1＠student.unimelb.edu.au 10 Jul '22

10 Jul '22

External Email - Use Caution Dear FreeSurfer developers, I'm attempting to run recon-all with the longitudinal stream, but one subject (out of >500) fails recon-all (I've re-started many times). The cross-sectional and base (i.e. steps 1 and 2 of the longitudinal processing) have completed successfully; it's this final step that has the error. It appears that the error lies in mri_cc. The final lines of the recon-all.log are below: #-------------------------------------- #@# CC Seg Wed Jun 29 14:56:47 AEST 2022 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V Y will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta reading aseg from /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz error: No such file or directory error: mri_cc: volume /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz already has CC in it. Run with -force to reprocess (not recommended) @#@FSTIME 2022:06:29:14:56:47 mri_cc N 7 e 0.39 S 0.00 U 0.38 P 99% M 21240 F 0 R 1813 W 0 c 6 w 5 I 0 O 0 L 64.77 63.93 63.78 @#@FSLOADPOST 2022:06:29:14:56:47 mri_cc N 7 64.77 63.93 63.78 Linux spartan-bm112.hpc.unimelb.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Thu Jul 8 02:53:40 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V Y exited with ERRORS at Wed Jun 29 14:56:47 AEST 2022 Freesurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b (I have also attempted with version 7.1.0 with identical results) Platform: centos7_x86_64 Recon-all.log: attached. With thanks, Rebecca

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Problem with sxconcat-sess
by Shapiro, Noah Lorenz 10 Jul '22

10 Jul '22

Hello, I am trying to concatenate my functional data with the following command (Ps: I am relatively new to FreeSurfer): sxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_R -contrast bilateral_isthmuscingulate_bold_config -o DMN_Right. I get an error that says the dof file cannot be found for my 26 scans in $SUBJECTS_DIR. However, running: find . -name "dof" The dof file was created for 12 scans. I used the same analysis pipeline for all the scans. I searched the mailing list, and haven't found anything that could help my problem. Any idea why the dof was not created for all scans? How can I create the dof for the remaining scans? Please let me know if you need further details. I am using Freesurfer version 6.0.0. Any help is very much appreciated. Please find the terminal output below. Best wishes, Noah actrumri[0]:RECONS$ echo $SUBJECTS_DIR /autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_R -contrast bilateral_isthmuscingulate_bold_config -o DMN_Right DMN_Right/PCC_Bold_R/log/isxconcat.log ERROR: cannot find /autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_R/dof actrumri[0]:RECONS$ find . -name "dof" ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_R/dof actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_L -contrast bilateral_isthmuscingulate_bold_config -o DMN_Left DMN_Left/PCC_Bold_L/log/isxconcat.log ERROR: cannot find /autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_L/dof actrumri[0]:RECONS$ find . -name "dof" ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_R/dof actrumri[0]:RECONS$

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Tksurfer Error
by Rachel Wagner 10 Jul '22

10 Jul '22

External Email - Use Caution Hello, I am attempting to paint my spm functional data onto freesurfer’s anatomical image. I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg register.dat And got this error: Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary" Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories: ./library ./tix8.1 ./library ./tix8.1 /usr/pubsw/packages/tcltktixblt/current/lib/tix8.1 How can I fix this error? Thanks, Rachel

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mri_concat killed
by Benjamin Deck 10 Jul '22

10 Jul '22

External Email - Use Caution Hi there, I am attempting to concat a number of volume files that are filled cortical ribbons from a series of label files. My workflow is to take the following steps: *Convert overlay file to label file* mri_vol2label --i ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${hemi}.${netMaskName}_native.mgh \ --id 1 \ --l ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${hemi}.${netMaskName}_native.label \ --surf ${sub} ${hemi} white \ --dilate 2 mri_label2label --srclabel ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${hemi}.${netMaskName}_native.label \ --s ${sub} \ --hemi ${hemi} \ --trglabel /${subDir}/${sub}/label/li2019/${hemi}.${netMaskName}_native.label \ --regmethod surface *Convert label to volume * mri_label2vol --label /${subDir}/${sub}/label/li2019/${hemi}.${netMaskName}_native.label \ --identity \ --fill-ribbon \ --subject ${sub} \ --hemi ${hemi} \ --o /${subDir}/${sub}/mri/li2019_vols/${hemi}.${netMaskName}_native.mgz *Finally concatenate the vols together* mri_concat --f rois.txt --o yeo2011_nat.mgz --sum ninputs = 104 Checking inputs nframestot = 104 Allocing output Done allocing Killed Not sure why this is being killed. OS: WSL2 Ubuntu FS version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Thanks for your help! -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1YhK4K5F2roM94PXj8RhOckUkCKJ0E3EcVeEJ8IfNRgJUQ…> Virus-free. http://secure-web.cisco.com/1YLbrDWxmBkdEGq0tv_IFuOJQDM7x0wCDq8h35ylt8kjv2A… <https://secure-web.cisco.com/1MZHAAPhLAJ8ofUmsU3lV3kCeJvwetaDxZd4U6AuxDlSyz…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Segmentation Mistakes
by Wang, Yu 10 Jul '22

10 Jul '22

External Email - Use Caution Hello FreeSurfer Developers, I used the recon-all -s c1NT816 -i smwrc1NT816_screen_mpr.nii -no-ants-n4 -all command, and the script of recon-all did not shows any errors. But the segmentation of this shows very strange and the screenshot of FREEVIEW was attached in https://secure-web.cisco.com/1DiZCsT29ph0nxelagWzgxiK83DeI03n5r7jqcEK7snAAy… I have search for this mistake online, and I only find a similar one (https://secure-web.cisco.com/17rnPwV1D9noAjOEul8R2iNskGBej5a9MhpLH-Wq1n1UTw…) but it do not show the method about what would cause this problems and how to solve it. 1. FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 2. Platform: ubantu 20.04.4 3. uname -a: Linux sulu 5.4.0-113-lowlatency #127-Ubuntu SMP PREEMPT Wed May 18 15:12:18 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4. recon-all.log: see attached I will be appreciated if you can give me a hand with these problems. And looking forward to your reply. Thanks in advance, Yu

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Command Not Found
by Rachel Wagner 10 Jul '22

10 Jul '22

External Email - Use Caution Hello, Thank you for your help! I am trying to register my spm image and am getting the following error: developer@developer-VirtualBox:~$ kregister2 --s home --mov updated.mgz --regheader --reg register.dat --surf orig kregister2: command not found Is my path not set correctly? Thanks again, Rachel Wagner

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How to project SPM image
by Rachel Wagner 06 Jul '22

06 Jul '22

External Email - Use Caution Hello, I am trying to project my SPM nii image onto an anatomical image to project them onto a cortical surface in Freesurfer, to generate images which look like this: Fig. 4: Refining neuroanatomical treatment targets for addiction. | Nature Medicine<https://secure-web.cisco.com/1mejk3edpL22Nxd2a1vnicVV8HsoH4qBsXKIzfqDBspXAg…> Has anyone done this before and would be able to point me towards any resources to do so? Thank you, Rachel Wagner

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trac-all -prep -c ERROR
by Salar Dini, Elaheh 03 Jul '22

03 Jul '22

External Email - Use Caution Dear experts, I am running TRACULA for 90 subjects. Exceptionally, for one of the subjects, I get the following error in -prep step: ((INFO: Distances between consecutive points in test subject's space are 10 13 12 13 13 12 WARN: Could not find satisfactory control point fit - try 17034 Writing output files to /home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_* Writing spline volume to /home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_cpts_7.nii.gz Segmentation fault (core dumped) Linux tauruspet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Jun 29 10:31:11 EDT 2022)) I am attaching the log file as well: https://secure-web.cisco.com/1SmnY7WYnV1XRZV1hzFK0-fljtz5hTgSEDuVurOZOZqB22… On a quick look, aparc+aseg seems to be properly done. Will you please help me to troubleshoot this if possible? Thank you, Ela

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Research Assistant Opening at Human iEEG Lab in NY
by Tostaeva, Gelana 30 Jun '22

30 Jun '22

External Email - Use Caution Hello all, Please circulate this opportunity to any interested parties. Sorry for cross-posting. Thank you! ------------------------------------------- The human intracranial EEG Laboratory at The Feinstein Institutes for Medical Research – Hofstra Northwell School of Medicine in New York is looking for one research assistant with earliest start date in July 2022. The successful candidate will help with the lab’s research into (1) improving the identification of functional and pathological brain regions in individuals suffering from epilepsy, (2) the neural mechanisms of cognition, and (3) characterization of macroscale human brain networks. The lab works exclusively with patients being evaluated for epilepsy surgery using methods such as invasive stereo EEG and electrocorticography recordings (iEEG, ECoG), anatomical MRI, fMRI, DTI, and direct electrical brain stimulation. The position is computationally focused, and responsibilities include analysis of neural, imaging, and behavioral data using existing scripts (Matlab and Python), further development of analysis scripts (depending on proficiency with coding and signal processing), and database managing. However, responsibilities will also include assisting with the collection and analysis of the aforementioned data, project management, assistance with preparing progress reports and grant applications, and helping to present lab findings at conferences and in journals. The relative weighing of responsibilities can also be adjusted depending on interest of the applicant. In addition, if there is interest, the RA will have her/his own scientific project with dedicated time to work on it. Past research assistants in the lab have presented their work at clinical and basic research conferences, co-authored lab publications, and are working on first author publications. They have gone on to medical schools or PhD programs after spending 1-3 years in the lab. This unique position will expose the successful applicant to basic and clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. The location of the institute allows living either in the suburban neighborhoods of Long Island, or in vibrant Brooklyn or Queens. Some employees also commute from Manhattan. It is a great opportunity for recent post-bacs interested in medical school or graduate school in neuroscience/biomedical engineering. ------------- Qualifications ------------- Minimum: - B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, biomedical engineering, computer science, physics) - 1 year commitment - Experience with at least one programming language (MATLAB, R, or Python) Desirable: - 2-year commitment preferred - Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data - Previous experience working with patients - Previous work in a research laboratory that shows evidence of independent scholarship, problem solving, and motivation For more information about the position please send your CV along with your questions to Dr. Stephan Bickel (sbickel(a)northwell.edu) and Dr. Ashesh Mehta (amehta(a)northwell.edu) We are looking forward to hearing from you! The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Freesurfer June 2022