Freesurfer

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30084 discussions

Re: [Freesurfer] recon-all -long erros
by Hoopes, Andrew 09 Jun '20

09 Jun '20

As for the --preserve=timestamps error, this is a bug on osx. This will be fixed in the next 7.1 patch, but in the meantime, you can fix this manually via: cd $FREESURFER_HOME/bin sudo rm rca-long-tp-init sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-lon… -o rca-long-tp-init sudo chmod +x rca-long-tp-init best Andrew On 6/9/20, 7:36 AM, "Martin Reuter" <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Jieyin, a couple things I noticed: 1) you call this: recon-all -long P0567/tp4 P0567/tpm -all this is not the way recon-all should be called. You need to specify a SUBJECTS_DIR under which all your time points exists usually you would have $SUBJECTS_DIR/me_tp1 $SUBJECTS_DIR/me_tp2 $SUBJECTS_DIR/me_tpm # (the base or subject-template) $SUBJECTS_DIR/me_tp1.long.me_tpm # (output of long stream) $SUBJECTS_DIR/me_tp2.long.me_tpm # (output of long stream) $SUBJECTS_DIR/you_tp1 $SUBJECTS_DIR/you_tp2 ... If you want a separate directory for each subject, you would need to specify that dir in SUBJECTS_DIR and then the names would just be tp1 tp2 tpm tp1.long.tpm etc. It could be that the / in the subject name messes things up! 2. The command that fails is: /Users/jif19007/Documents/PLING_dataset/MRI_raw/pilot_data/output_P0567 /tp4.long.tpm/mri cp -f --preserve=timestamps /Users/jif19007/Documents/PLING_dataset/MRI_raw/pilot_data/output_P0567 /tpm/mri/brainmask.mgz ./brainmask_tpm.mgz cp: illegal option -- - maybe the mac has problems with the --preserve flag? I don't know when this was added and whether it is really necessary. Currently I don't even know where this is called. Can't find it in recon-all. Maybe some sub-script? Best, Martin On Wed, 2020-05-20 at 19:28 -0400, Jieyin Feng wrote: > External Email - Use Caution > Dear FreeSurfer experts, > > I am running longitudinal processing with FreeSurfer 7.1.0 on MacOX > Catalina. > The dataset is 5 time points with T1 data. I tried to run a single > subject. So far it succeeded on Step 1 (recon-all at each time > point), and Step 2 (-base to build the template), all of them > reported successfully. But I failed at step3, recon-all -long, to > compare each timepoint with the template. > The log file is attached. > I tried to run several times with different timepoints data, all > reported the same stuff. My guess is at the last 9 row, reported that > the cp command incorrectly. But I still have no idea to fix it, or > maybe I need to go to freesurfer's script file? I have no idea... > > Thanks for you time and help in advance! > Stay safe and sound! > > Best, > Jieyin > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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lGI permutation and monte-carlo
by Avi Gharehgazlou 09 Jun '20

09 Jun '20

External Email - Use Caution Hi experts, Upon reading your 2018 paper (cited below) and following threads on the archives, I am aware that I should use permutation testing for lGI analyses rather than monte carlo at p<0.05. However, I have a few questions below that I would really appreciate your input on: 1. For permutation testing on lGI data, what are the CFT and cwp levels you recommend? Would it be appropriate for me to use CFT=1.3 and cwp=0.05? 2. Will you confirm my interpretation for permutation command line below? mri_glmfit-sim --glmdir lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir --perm 1000 2 abs --perm-resid --cwp 0.05 --2spaces --bg 1 Above command indicates that I used a cluster-forming threshold of p<0.01 and a cluster-wise significance threshold of p<0.05 - meaning that clusters are initially obtained using p<0.01 (CFT) but I report them in my paper if they meet additional cluster-wise probability of p<0.05 (cwp). Both are two-tailed (since I am using abs). Is this interpretation correct? 3. Would it be okay to correct with monte carlo using CFT=3 and cwp= 0.05 (below command line) instead of permutation testing for lGI data? mri_glmfit-sim --glmdir lh.ASDvsADHD.glmdir --cache 3 abs --cwp 0.05 --2spaces 3. I am not smoothing my lGI data (as lGI is a relatively smooth measure and to keep this consistent with the literature I have reviewed), however, after reading your 2018 paper, I wanted to ask if this is appropriate? Your paper recommends CFT<0.001 and FWHM>10mm for surface area analyses. Do I have to smooth lGI when doing a) permutation testing or b) monte carlo correction (steps 1 and 3 above)? If yes, what level of smoothness do you recommend? 4. After correcting with monte-carlo at p<0.05 - When I use the below command line to see my corrected results in freeview, I notice the significant cluster is gray rather than blue (I know it should be blue because I've ran this same analysis using QDEC). In order to see this cluster's true colour (and thus be able to interpret my results) do I have to change the threshold by clicking ‘show outline overlay’ then clicking ‘configure’ and setting the min value to 1.3? Is this the correct way of visualizing my corrected results? vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.pial:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.ocn.annot -viewport 3d reference Greve DN & Fischl B. 2018. False positive rates in surface-based anatomical analysis. NeuroImage. Thank you so much, Avi

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Permutation --perm-resid unrecognized
by Avi Gharehgazlou 09 Jun '20

09 Jun '20

External Email - Use Caution Hi experts, I am trying to run permutation test on my lGI data using the command line below but I get an error saying “ERROR: Flag --perm-resid unrecognized”. I've ran my mri_glmfit command line with flag --eres-save (see below) and have installed and made executable the new version of mri_glmfit-sim as instructed here: ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.… ) Will you please tell me how I can fix this? permutation command line I used: mri_glmfit-sim --glmdir lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir --perm 1000 4.0 abs --perm-resid --cwp 0.05 --2spaces --bg 1 mri_glmfit command line I used: mri_glmfit --y lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.mgh --fsgd fsgd.txt dods --glmdir lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir --surf fsaverage lh --C group.diff.mtx --C group-x-age.mtx --C group-x-SA.mtx --C group-x-IQ.mtx --C lgi.intercept.mtx --C maineffect.age.mtx --C maineffect.IQ.mtx --cortex --eres-save Also, is it okay to run the --eres-save flag with mri_glmfit regardless even if I decide to do another correction (i.e. monte carlo later later on) or would results get affected? Thank you so much for your support, Avi

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Re: [Freesurfer] Freesurfer Digest, Vol 192, Issue 35
by Natalie Caspari 09 Jun '20

09 Jun '20

External Email - Use Caution Can you unsubscribe me please from this list? <freesurfer-request(a)nmr.mgh.harvard.edu> schrieb am Do., 27. Feb. 2020, 18:01: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Setting up Freeview on Ubuntu Linux 18.04: freeview can't > find libpng12 (Tim Sch?fer) > 2. field inhomogeneities and eddy current correction evaluation > (Adam Rytina) > 3. Re: Setting up Freeview on Ubuntu Linux 18.04: freeview can't > find libpng12 (fsbuild) > 4. Issue with BBR and Applying CVS Warps to Diffusion Data > (Austin Patrick) > 5. mri_vol2surf produces invalid surface (Shuntaro Aoki) > 6. Segmentation problem (Marina Fern?ndez) > 7. Full analysis chain without Topology fix, Talairach check? > (HsuD3(a)mskcc.org) > 8. Re: Full analysis chain without Topology fix, Talairach > check? (Bruce Fischl) > 9. Job post: full-time research assistant in the lab of Dr. > Emily Finn, Dartmouth College (Emily S. Finn) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 26 Feb 2020 18:03:18 +0100 (CET) > From: Tim Sch?fer <ts+ml(a)rcmd.org> > Subject: Re: [Freesurfer] Setting up Freeview on Ubuntu Linux 18.04: > freeview can't find libpng12 > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1495674409.723727.1582736598420(a)ox.hosteurope.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Tim, > > try: > > wget > http://mirrors.kernel.org/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1u… > sudo dpkg -i libpng12-0_1.2.54-1ubuntu1_amd64.deb > > More details at > https://www.xsmd.org/brain/2019/06/19/freeview-libpng12-so-0-missing-under-… > > Best, > > Tim > > > -- > Dr. Tim Sch?fer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > > > On February 26, 2020 at 5:36 PM "Harrigan, Timothy P." < > Timothy.Harrigan(a)jhuapl.edu> wrote: > > > > > > External Email - Use Caution > > > > HI, > > I'm setting up freeview on a Linux 18.04 system and running through the > instructions in > > https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall > > > > I got through to Example 4: "View the output volumes..." and got the > error below. > > > > harritp1@TPHTVB:~/FSSubjects$ freeview > > freeview.bin: error while loading shared libraries: libpng12.so.0: > cannot open shared object file: No such file or directory > > > > It looks like I need to either set up an environment variable, or > install that specific graphics library. I did an install of the latest > version of libpng: i. e. sudo apt-get install -y libpng-dev but that > didn't fix the problem. > > > > Have you dealt with this? > > > > Thanks > > Tim > > > > > > Timothy P. Harrigan ScD > > Research and Exploratory Development Division > > Johns Hopkins University Applied Physics Laboratory > > Phone: 240-228-5943 > > Cell/Text: 240-280-9444 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 2 > Date: Wed, 26 Feb 2020 18:56:41 +0000 > From: Adam Rytina <adam.rytina(a)outlook.cz> > Subject: [Freesurfer] field inhomogeneities and eddy current > correction evaluation > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > AM0PR0602MB3377830AE274DC1CCD6A42B09AEA0(a)AM0PR0602MB3377.eurprd06.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-2" > > External Email - Use Caution > > Hello all, > > how can I evaluate the field inhomogeneities and eddy current correction I > performed on my DWI images? Does any metric exist to do so? > > Thanks a lot in advance > Regards > Adam >

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mris_preproc label file not found
by Diana 09 Jun '20

09 Jun '20

External Email - Use Caution Dear experts, I am preparing my data for longitudinal statistical analysis following the steps in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics#LinearMixe…. I try running the following comand : mris_preproc --qdec-long qdec/long.qdec.table-test.dat --target fsaverage --hemi lh --meas area --out output/lh.area.stack.mghmris_preproc --qdec-long qdec/long.qdec.table-test.dat --target fsaverage --hemi lh --meas area --out output/lh.area.stack.mgh but it crashes because it looks for /fsaverage/label/lh.cortex.label How can I create this label file? Thank you very much in advance for your help, please find below the whole output. Best, Diana nsubjects = 25 INFO: turning on jacobican correction tmpdir is output/tmp.mris_preproc.21054 /home/neuroimagen/AnalisisLongitudinalLMM Log file is output/lh.area.stack.mris_preproc.log lun jun 8 17:41:42 CEST 2020 setenv SUBJECTS_DIR /home/neuroimagen/AnalisisLongitudinalLMM/ cd /home/neuroimagen/AnalisisLongitudinalLMM /usr/local/freesurfer/bin/mris_preproc --qdec-long qdec/long.qdec.table-test.dat --target fsaverage --hemi lh --meas area --out output/lh.area.stack.mgh Linux localhost 4.4.0-179-generic #209-Ubuntu SMP Fri Apr 24 17:48:44 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is output/tmp.mris_preproc.21054 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/25 100_001.long.100 lun jun 8 17:41:42 CEST 2020 -------------- ----------------------- mri_surf2surf --srcsubject 100_001.long.100 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval output/tmp.mris_preproc.21054/100_001.long.100.1.mgh --sval /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.area --jac --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /home/neuroimagen/AnalisisLongitudinalLMM/ cd /home/neuroimagen/AnalisisLongitudinalLMM mri_surf2surf --srcsubject 100_001.long.100 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval output/tmp.mris_preproc.21054/100_001.long.100.1.mgh --sval /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.area --jac --sfmt curv --noreshape --cortex sysname Linux hostname localhost machine x86_64 user neuroimagen srcsubject = 100_001.long.100 srcval = /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.area srctype = curv trgsubject = fsaverage trgval = output/tmp.mris_preproc.21054/100_001.long.100.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.sphere.reg Loading source data Reading curvature file /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.area Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /home/neuroimagen/AnalisisLongitudinalLMM//fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (149877) Reverse Loop had 29625 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done No such file or directory mri_surf2surf: could not open label file /home/neuroimagen/AnalisisLongitudinalLMM//fsaverage/label/lh.cortex.label nTrg121 = 141330, nTrgMulti = 22512, MnTrgMultiHits = 2.31596 nSrc121 = 115191, nSrcLost = 0, nSrcMulti = 34686, MnSrcMultiHits = 2.2567 Reading target space mask label lh.cortex.label Invalid argument

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World's leading AI Company for brain imaging is recruiting brain imaging scientists.
by 马健 09 Jun '20

09 Jun '20

External Email - Use Caution Full/Part-time MR Imaging Analysis Scientist Overview World's leading AI Company for brain imaging is recruiting brain imaging scientists.  With the team’s strong background in scientific research and medical industry, it focuses on the precise assessment and diagnosis of various brain diseases by using advanced medical imaging techniques. We accepted part-time applications. Responsibilities ·         Professional in imaging data analysis in Diffusion MRI, DTI, SWI (QSM), fMRI et al.  ·         Responsible for the project of analysis algorithm design for  MR image ·         Build the pipeline for imaging algorithm and coding technical support for the imaging  analysis product of company ·         Corresponding technical documents writing Required Qualifications: ·         Advanced knowledge of MR imaging ·         Familiar with central nervous system ·         Familiar with radiological image quality metrics ·         Familiar with processing tools such as SPM,FSL,3D slicer, Radiant, ITK, VTK for radiological image ·         Strong programming skills in languages such as Python, C++ , MATLAB Preferred Qualifications: ·         Good written and verbal communication skills ·         Ability to work both independently and collaboratively on assigned projects Minimum Education ·         Ph.D. in biomedical engineering, medical physics, neurology, computer sciences or related scientific field required. Minimum Experience ·         One (1) year's research or work experience in medical image analysis is required.   Please send your CV to Dr. Pauil Ma, pauil.ma(a)szdrbrain.com.   

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Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz
by Zeng, Qi 08 Jun '20

08 Jun '20

External Email - Use Caution Hi, I conducted longitudinal segmentation of both hippocampus and amygdala from running segmentHA_T1_long.sh. But is it possible for me to segment only the hippocampus region "mgz" from the stored [lr]h.hippoAmygLabels-T1.long.v21.mgz ? Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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samseg with subfields
by Sneha Pandya 08 Jun '20

08 Jun '20

External Email - Use Caution Dear experts, Is it possible to run subfield analysis (hippcampal subfields, amygdalar, thalamic nuclei, and brainstem structures) when we only run samseg on our dataset? Thank you, Sneha

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Fwd: Welcome to the "Freesurfer" mailing list
by Paolo Zanotti Fregonara 08 Jun '20

08 Jun '20

External Email - Use Caution Hi Would it be possible to post this job offer to the mailing list? Thanks Paolo ---------- Forwarded message --------- From: <freesurfer-request(a)nmr.mgh.harvard.edu> Date: Mon, Jun 8, 2020 at 10:30 AM Subject: Welcome to the "Freesurfer" mailing list To: <pzfregonara(a)gmail.com> Welcome to the Freesurfer(a)nmr.mgh.harvard.edu mailing list! To post to this list, send your email to: freesurfer(a)nmr.mgh.harvard.edu General information about the mailing list is at: https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer If you ever want to unsubscribe or change your options (eg, switch to or from digest mode, change your password, etc.), visit your subscription page at: https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer/pzfregonara%40g… You can also make such adjustments via email by sending a message to: Freesurfer-request(a)nmr.mgh.harvard.edu with the word `help' in the subject or body (don't include the quotes), and you will get back a message with instructions. You must know your password to change your options (including changing the password, itself) or to unsubscribe. It is: Paolofreesurfer73 Normally, Mailman will remind you of your nmr.mgh.harvard.edu mailing list passwords once every month, although you can disable this if you prefer. This reminder will also include instructions on how to unsubscribe or change your account options. There is also a button on your options page that will email your current password to you.

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gtmseg getSignalBehindHead ERROR (no slices behind head)
by Boris Rauchmann 08 Jun '20

08 Jun '20

External Email - Use Caution Dear FS experts, In my dataset I have 4 subjects where the T1 was acquired, planning the FOV very close to the occipital lobe. I guess that triggers the error: getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7 slices behind head! ERROR: xcerebralseg and results in gtmseg exited with errors. How can I fix this? Best regards, Boris

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