Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

Still unsure how to create my 3g4v matrix
by nellie 01 Dec '15

01 Dec '15

Hi expert, Thank you for your reply. I had read the example tables, but I'm still not sure how to alter them into my analysis.Can you help me to check the matrix I designed and point out my mistakes? Thanks in advence. 3 classes ( A / B / C group) and 4 variables (gender, age, education, and Moca test score). group.diff.mtx 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 group-x-gender.mtx 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 group-x-age.mtx 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 group-x-education.mtx 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 group-x-moca.mtx 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 group-x-gender-x-age-x-education.mtx 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 group-x-gender-x-age-x-education-x-moca.mtx 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 group.diff.mtx also can write as: 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 group-x-age.mtx aslo can write as: 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 . Wishes, Li > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Freesurfer digest..." > > >Today's Topics: > > 1. Re: How to create a 3g4v matrix (Lee Tirrell) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Mon, 23 Nov 2015 10:27:42 -0500 (EST) >From: Lee Tirrell <ltirrell(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] How to create a 3g4v matrix >To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >Message-ID: > <alpine.LRH.2.20.1511231020130.5623(a)vermis.nmr.mgh.harvard.edu> >Content-Type: text/plain; charset="iso-8859-7" > >Hi Li, > >You can find some example FSGD tables here, which you can alter to fit your >analyses. > >https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > >Best, >Lee > >On Sun, 22 Nov 2015, nellie wrote: > >> >> Hi Freesurfer Experts, >> >> I?m a new user of Freesurfer, and I learn how to use this software mainly through Wiki. When I came to the step of using GLM to compare group differences, I was confused on the design of 3g4v matrix. In my study, there were 3 classes ( >> A / B / C group) and 4 concomitant?variables (gender, age, education, and Moca test score). It?s supposed to be 15 regressors in this design, but I don?t know how to use the numbers (like 1, -1, 0, 0.5, -0.5, etc.) to create a correct >> matrix. I wonder if you could provide a 3g4v matrix in detail for me. I?ll be grateful if you can help. I hope I?m not bothering you too much, and I?m looking for your reply. >> >> Best wishes, >> >> Li? >> >> >> >> ? >> >> >> > >------------------------------ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >End of Freesurfer Digest, Vol 141, Issue 40 >******************************************* > > >The information in this e-mail is intended only for the person to whom it is >addressed. If you believe this e-mail was sent to you in error and the e-mail >contains patient information, please contact the Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error >but does not contain patient information, please contact the sender and properly >dispose of the e-mail. >

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Sign options of Monte Carlo simulation in QDEC
by Karl Liu 01 Dec '15

01 Dec '15

Dear Freesurfer experts: we would appreciate if anyone could advise on the sign choice of Monte Carlo simulation, a question we posted 2 days ago. In examining QDEC results of a contrast of interest, we noticed the results are mainly in cold color (blue), with only two small clusters in warm color (red). When I proceeded with Monte Carlo simulation, if I chose the abs as the sign option in simulation, then no clusters survived. In contrast, some clusters would remain, if I chose the neg sign. Because the uncorrected results were mainly in cold color, it seems reasonable to me to use negative only in the simulation. But I am wondering how the option of abs/neg/pos leads to the disparities and will you please elaborate how the simulation works based on abs/neg/pos. Can I state that my results survived the cluster-level correction if I chose the neg sign in simulation? Thank you very much. Karl

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'mkdir' error during the segmentation of hippocampal subfields using FreeSurfer 6 [2nd request for help]
by Fengji Geng 01 Dec '15

01 Dec '15

Dear FreeSurfer Users, I sent an email to this maillist a couple of weeks ago asking help for the error that I encountered after running 'recon-all -s ${Mysubject} -hippocampal-subfields-T1' with freesurfer 6. The content of this email is attached below. Since then, my colleague and I have been working on figuring out where the error is from, but we got two more questions here: First, is it possible that we can set the tmpdir to /tmp or something else globally? How can I do this? Second, is it possible to fix test for '-e/scratch' to test for '-dw/scratch', which is a directory writable by current user? Any comments and suggestions are appreciated. Thanks in advance! Fengji Previous email: I was trying to segment hippocampal subfields using FreeSurfer 6 with data that have already undergone the FreeSurfer 5 pipeline recon-all -all. According to the usage described on the webpage of HippocampalSubfields (http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) I ran the command: recon-all -s ${Mysubject} -hippocampal-subfields-T1 Then the following errors occurred. It seems that the program 'segmentSubjectT1_autoEstimateAlveusML (line 113)' was trying to make a directory in a Read-only place. But the error message did not indicate where this place was. I have tried to look codes in 'run_ segmentSubjectT1_autoEstimateAlveusML.sh" . But it does not have this information either. As segmentSubjectT1_autoEstimateAlveusML is a binary file, I could not dig out any more info. Does anyone know how to solve this error? Or know where the program was trying to mkdir? Here begins the error message: hippocampus:/<2>hippocampus/HMN/data/FG_Temp: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Wed Nov 18 21:57:45 EST 2015 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib Warning: application is running on a locale different from the original platform locale. Error using mkdir Read-only file system Error in segmentSubjectT1_autoEstimateAlveusML (line 113) MATLAB:MKDIR:OSError #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Wed Nov 18 21:57:50 EST 2015 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib Warning: application is running on a locale different from the original platform locale. Error using mkdir Read-only file system Error in segmentSubjectT1_autoEstimateAlveusML (line 113) -------------------------------------------------------------------------------------------------------- ----- Fengji

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OPPORTUNITY OF FULL-TIME POSTDOCTORAL FELLOWSHIP AT THE UNIVERSITY OF SÃO PAULO, BRAZIL
by Neuroimagem IPQHCFMUSP - LIM21 01 Dec '15

01 Dec '15

One postdoctoral position is available within the Laboratory of Psychiatric Neuroimaging (LIM21) (www.neuroimagem.org.br/) at the University of São Paulo Medical School, Brazil, directed by Geraldo F. Busatto, Ph.D. Candidates should send a message to neuroimagem.ipq(a)hc.fm.usp.br with his/her CV and a letter of support. Deadline: 13 Dec 2015 *JOB DESCRIPTION* We are looking for a full-time researcher with previous experience in the use of software for the analysis of neuroimaging data. This post-doctoral fellow will be requested to work mainly with data acquired using resting-state functional magnetic resonance imaging methods (rs-fMRI) to evaluate patterns of functional connectivity in the brain. In our project, funded by the *FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO, BRAZIL* (FAPESP), such brain imaging data is being acquired in groups of cognitively-intact elderly individuals, patients with Alzheimer´s disease (AD), and patients with mild cognitive impairment (MCI). Pre-processing steps will be carried out using the software Analysis of Functional NeuroImages (AFNI), while the actual processing of data will be conducted using Matlab-based programs. The work will also involve use of software to evaluate the diagnostic accuracy to distinguish between AD, MCI and healthy elderlies, generating multivariate classifiers based on machine-learning methods (support vector machine). With such strategy, we aim to identify which are the functional connectivity characteristics in the brain that are most critical for the progression from normal cognition to MCI and then to AD. The post-doctoral fellow should have knowledge about the acquisition and analysis of fMRI data and other neuroimaging modalities. We aim to bring an individual with abilities to carry out, independently, analyses and organization of computational brain imaging data, interaction with other researchers involved in the same project, and participating in the writing up of scientific papers. These characteristics are expected to boost the scientific productivity from the funded project, both quantitatively and qualitatively. The professional will also have the opportunity to interact with scientists who are at the forefront of technologies for amyloid imaging in the brain, and data will be combined with fMRI analyses in the same elderly subjects evaluated with those two imaging technologies. The post-doctoral fellow will have the opportunity to practice abilities in analysing data of a challenging scientifc project, and he/she will be expected to establish and use optimized processing pipelines for the analysis of rs-fMRI data and other neuroimaging modalities. *Requirements* - Completed PhD in areas related to computer sciences, neuroscience, neurology or psychiatry - Research interest and brain imaging applied to research studies of brain aging - Previous experience in the usage of processing and statistical analysis methods for research studies applied to magnetic resonance imaging studies of the brain. best regard *Laboratory of Psychiatric Neuroimaging - HCFMUSP*

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Create surface overlay from p-values
by Bronwyn Overs 30 Nov '15

30 Nov '15

Hi Freesurfer mailing list, Using an external software package we have completed of analysis for the vtx-wise thickness data extracted from freesurfer. We now have a p-value array containing one value for each vtx, and we would like to map this back onto the brain surface. Is there a way to create a .mgh overlay from our array of p-values using fsaverage as the subject? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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FSGD File Formatting Error
by Shady El Damaty 30 Nov '15

30 Nov '15

Hi Freesurfers, I'm having some issues running mri_glmfit using a simple custom GLM file. I've double checked to make sure the subject session file passed to isxconcat-sess is the same as the fsgd file and also checked the formatting corresponds with what is posted online however I keep getting the same error: ERROR: gdfReadV1: Input line 1, subjid = A02217-w2 Found 43 variables, expected. 1 FSGDF Format Error: file = /Users/seldamat/Dropbox/Projects/ADS/data/ads.emostroop.marketing/new.exposure.fsgd, tag=Input ERROR: cannot find glm-exposure My fsgd file is attached. Please any help would be greatly appreciated on this time sensitive matter. Thank you, Shady On Thu, Nov 26, 2015 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > 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. voxel value scaling (Rockers, Elijah D.) > 2. Re: voxel value scaling (Douglas Greve) > 3. Re: voxel value scaling (Rockers, Elijah D.) > 4. Re: Error - extracting percent signal (Douglas Greve) > 5. Re: bring volumes to fsaverage space (Andrew Bock) > 6. FS v.6.0 (Th?c Trinh) > 7. recon-all with more than 10 inputs (???) > 8. Re: Multiple comparisons to confirm atrophy (Anderson M. Winkler) > 9. report a bug (salvatoreandrea.92(a)libero.it) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 25 Nov 2015 17:08:28 +0000 > From: "Rockers, Elijah D." <edrockers(a)houstonmethodist.org> > Subject: [Freesurfer] voxel value scaling > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <5655EB0C.1000309(a)houstonmethodist.org> > Content-Type: text/plain; charset="utf-8" > > I am interested in finding a way to apply a slope scaling factor to the > voxel values in a NIfTI image. > > I have done this in MATLAB and PMOD so far, but for some reason both > methods change the origin or otherwise distort the dimensions of the > image and render it impossible for me to process further. > > Something that simply scales the values without touching the header (or > at least as little as possible) would be great. Is anything like this > out there? > > Thanks, > > Eli > > Houston Methodist. Leading Medicine. > > Ranked by U.S.News & World Report as one of America's "Best Hospitals" in > 11 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work > For?" list 10 years in a row. Designated as a Magnet hospital for > excellence in nursing. Visit us at houstonmethodist.org. Follow us at > twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston > Methodist Hospital and/or its relevant affiliates and may contain > restricted and privileged material for the sole use of the intended > recipient(s). Any review, use, distribution or disclosure by others is > strictly prohibited. If you are not the intended recipient (or authorized > to receive for the recipient), please contact the sender and delete all > copies of the message. Thank you. > > > > ------------------------------ > > Message: 2 > Date: Wed, 25 Nov 2015 12:54:23 -0500 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] voxel value scaling > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <5655F5CF.8050907(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > You can use fscalc, something like > fscalc input.nii mul 10 -o output.nii > I think you can use fslmaths as well > > On 11/25/15 12:08 PM, Rockers, Elijah D. wrote: > > I am interested in finding a way to apply a slope scaling factor to the > > voxel values in a NIfTI image. > > > > I have done this in MATLAB and PMOD so far, but for some reason both > > methods change the origin or otherwise distort the dimensions of the > > image and render it impossible for me to process further. > > > > Something that simply scales the values without touching the header (or > > at least as little as possible) would be great. Is anything like this > > out there? > > > > Thanks, > > > > Eli > > > > Houston Methodist. Leading Medicine. > > > > Ranked by U.S.News & World Report as one of America's "Best Hospitals" > in 11 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work > For?" list 10 years in a row. Designated as a Magnet hospital for > excellence in nursing. Visit us at houstonmethodist.org. Follow us at > twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. > > > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston > Methodist Hospital and/or its relevant affiliates and may contain > restricted and privileged material for the sole use of the intended > recipient(s). Any review, use, distribution or disclosure by others is > strictly prohibited. If you are not the intended recipient (or authorized > to receive for the recipient), please contact the sender and delete all > copies of the message. Thank you. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 25 Nov 2015 18:01:37 +0000 > From: "Rockers, Elijah D." <edrockers(a)houstonmethodist.org> > Subject: Re: [Freesurfer] voxel value scaling > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Cc: "Pascual, Maria B." <BPascual(a)houstonmethodist.org>, "Xue, Zhong" > <ZXue(a)houstonmethodist.org> > Message-ID: <5655F781.6000609(a)houstonmethodist.org> > Content-Type: text/plain; charset="utf-8" > > Great thank you! > > On 11/25/2015 11:54 AM, Douglas Greve wrote: > > You can use fscalc, something like > > fscalc input.nii mul 10 -o output.nii > > I think you can use fslmaths as well > > > > On 11/25/15 12:08 PM, Rockers, Elijah D. wrote: > >> I am interested in finding a way to apply a slope scaling factor to the > >> voxel values in a NIfTI image. > >> > >> I have done this in MATLAB and PMOD so far, but for some reason both > >> methods change the origin or otherwise distort the dimensions of the > >> image and render it impossible for me to process further. > >> > >> Something that simply scales the values without touching the header (or > >> at least as little as possible) would be great. Is anything like this > >> out there? > >> > >> Thanks, > >> > >> Eli > >> > >> Houston Methodist. Leading Medicine. > >> > >> Ranked by U.S.News & World Report as one of America's "Best Hospitals" > in 11 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work > For?" list 10 years in a row. Designated as a Magnet hospital for > excellence in nursing. Visit us at houstonmethodist.org. Follow us at > https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHo… > and > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.facebook.com_Housto… > . > >> > >> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston > Methodist Hospital and/or its relevant affiliates and may contain > restricted and privileged material for the sole use of the intended > recipient(s). Any review, use, distribution or disclosure by others is > strictly prohibited. If you are not the intended recipient (or authorized > to receive for the recipient), please contact the sender and delete all > copies of the message. Thank you. > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… > . If the e-mail was sent to you in error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > > > ------------------------------ > > Message: 4 > Date: Wed, 25 Nov 2015 13:03:39 -0500 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Error - extracting percent signal > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <5655F7FB.8010801(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > It looks like the ces input is from a surface-based analysis. If you're > label is already on the surface, then no need to do the label2vol step. > If it is in the volume, then you'll need to transfer it to the surface > with mri_label2label with the --paint option > doug > > On 11/24/15 12:14 PM, Danielle Miller wrote: > > Hello freesurfer experts, > > > > I am trying to extract an average percent signal change from a > > functional roi label I created in tkmedit using fsaverage. I followed > > previously discussed methods: > > > > 1) mri_label2vol --label <name of label> --temp > > fsaverage/mri.2mm/orig.mgz --regheader fsaverage/mri/orig.mgz --o > > <name of label mask> > > > > 2) I checked (tkmedit fsaverage orig.mgz -overlay <label mask> > > -fminmax .5 1) and the label looked fine > > > > 3) I ran mri_segstats --i ces.nii.gz --seg <label mask from above> > > --id 1 --avgwf ces.label.dat > > ces.nii.gz is the file from my group analysis (isxconcat-sess) using > > the correct contrast > > It returns with this error: > > ERROR: dimension mismatch between input volume and seg > > input 163842 1 1 > > seg 76 76 93 > > > > Is there something I am doing wrong here? > > > > Also of note I tried using the following commands: > > 1) funcroi-config -label <label mask created from above mri_label2vol> > > -analysis <analysis directory> -roi <name of roicfg file> > > > > 2) funcroi-sess -sf sessid - roi <roicfg file from above> > > But this returns with this error: > > ERROR: cannot find > > > /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_001_recon/label/label_lh_ACC_correct_mask.mgz > > > > > > Any suggestions would be extremely helpful. > > > > Thanks, > > Danielle > > -- > > Ph.D. Program in Behavioral Neuroscience > > Boston University School of Medicine L-815 > > 72 E. Concord St > > Boston, MA 02118 > > > > > > VA Boston Healthcare System Jamaica Plain > > Memory Disorders Research Center > > 150 South Huntington Ave D11-103 > > Boston, MA 02130 > > OFFICE:(857) 364-2130 > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Re: [Freesurfer] Freesurfer Digest, Vol 141, Issue 48
by Bishesh Khanal 30 Nov '15

30 Nov '15

> Message: 14 > Date: Mon, 30 Nov 2015 09:32:54 -0500 > From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] long run fails for new time-point when > removing a tpt that was added with -addtp option > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <565C5E16.3060301(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi Bishesh, > > Disclaimer up front: > You probably know that adding time points without re-creating the base > is dangerous (as you bias you analysis, because not all time points are > treated the same). > > Thanks Martin. Yes I understand that but I'm trying to use recon-all in a different setting. For e.g. if I want to compare FreeSurfer results on repeat scans: new1 and new2 both taken on the same day, I understand that ideally one would do two different long runs by including new1 and new2 separately during the creation of base template and then compare the results. However, in my case instead of just new1 and new2, I have several of them that are simulated using different methods and these simulated images will be very close to the images that were already used during the base template creation. So I did not want to recreate the base template for each of these several cases. I want to analyse results on these new1, new2, new3, ..., newN simulated scans of the "same time-point" image but with different methods without recreating the base-template and providing the identical scenario for each of these new1, new2, ..., newN images in long-run. > Now here is why you see the error. > The way a new time points get added to an existing base is this: > 1. register the new time point's norm.mgz to the base norm.mgz (using > mri_robust_register and creates the lta files in mri/transforms) > 2. create a new temporary base norm.mgz from all time points and diff > with existing base norm.mgz > 3. report difference (the idea is to decide if the difference is small > then everything is fine and if it is large, recommend to re-run the base > from scratch, this is not implemented yet and you only see output and it > will always go through) > 4. add the new time point id to the list in base/base-tps > > So for step 3 it needs the norm.mgz from all other time points, to > re-create a temporary norm in the base. > > Now, how can you achieve what you want. I can think of two options: > - edit the base-tps and remove the line with new1 > this should work, the additional transforms to and from new1 (in > base/mri/transforms) can be left behind as they will not be used (you > can also delete those if you like) > - create two copies of the original base (before adding any time > points), then add each time point to each of the two copies. This is > absolutely safe as you make sure that new1 does not affect anything when > adding new2. > Yes if I had only two tpts, copying could be reasonable too, but I have few more, so I'm now considering the first option. Or a quicker way for me could be to temporarily comment out steps 2 and 3 you mentioned above. Could you tell me where in recon-all I could do that ? Thanks, Bishesh > > Anyway, I don't see why anyone would want to do what you are trying to > do, but good luck. > > Best, Martin > > On 11/30/2015 05:53 AM, Bishesh Khanal wrote: > > Hello, > > I had run a longitudinal run by creating a base template with a set of > > time-point scans (tpts). I wanted to add a new tpt (say new1) without > > recreating the base template, hence I used the option -addtp in the > > recon-all -long run. Later on, I no longer needed the results of the > > long run for new1. So I removed the relevant directories for new1 > > (i.e. new1 and new1.long.baseid). > > > > Now I have another tpt (say new2) for which I want a -long run without > > recreating the base template. So I did the same thing as before i.e. > > first a cross run for new2 (which worked fine) and then a long-run > > with -addtp option. However, the long-run for new2 failed with an > > error that it cannot find $SUBJECTS_DIR/new1/mri/norm.mgz > > > > I realize that although I had removed the relevant directories of > > new1, it is still listed in the file $SUBJECTS_DIR/baseid/base-tps. > > However, I do not understand why norm.mgz of new1 is needed by > > recon-all for a long run on new2 when I did not want FreeSurfer to use > > either of new1 or new2 to recreate the base. Ideally, I would want to > > run long run on new1 and new2 under identical conditions. In other > > words, I do not want long-run on new2 tpt to require results from long > > run on new1 tpt. Should it not be the expected behaviour when I am not > > using new1 and/or new2 to create the base template ? > > And, is there a way to do achieve what I want to without manually > > deleting the new1 from the list in the file > > $SUBJECTS_DIR/baseid/base-tps ? > > > > P.S. Initially, the -addtp option had not worked and I had to do the > > following to make it work: > > > > The FreeSurfer version: 5.3.0. Getting around a know bug. in recon-all > > in the following block (around line 6148) > > > > if ( ! $found_tpNid ) then > > echo "ERROR: $tpNid is not in > > ${longbasedir}/${BaseSubjsListFname}" > > echo "" > > exit 1 > > endif > > > > > > replaced the first line (if statement) with: > > > > if ( ! $found_tpNid && ! $DoAddTp ) then > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu > >

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R: Re: report a bug
by salvatoreandrea.92＠libero.it 30 Nov '15

30 Nov '15

I have around 2 Gb of total RAM. Isn't that sufficient to run recon-all? If it is not, do you know whether there is a way to split up the process? ----Messaggio originale---- Da: theniels(a)gmail.com Data: 27-nov-2015 17.24 A: "salvatoreandrea.92(a)libero.it"<salvatoreandrea.92(a)libero.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] report a bug Hi - sounds like it's running out of memory and getting killed. How much RAM do you have? On Thu, Nov 26, 2015 at 1:21 PM, salvatoreandrea.92(a)libero.it <salvatoreandrea.92(a)libero.it> wrote: Hi! - I am using Ubuntu 14.4 (trusty). - This is my subject directory: /home/salvatore/freesurfer/subjects - This is the output of which recon-all (that is the tool I am trying to use): /home/salvatore/freesurfer/bin/recon-all - The command line that I run is recon-all -s /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis -i /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis/T1.nii.gz -all Following the error that I got after 12 hours of processing: sysname Linux hostname salvatore-HP-630-Notebook-PC machine x86_64 setenv SUBJECTS_DIR /home/salvatore/freesurfer/subjects cd /home/salvatore/freesurfer/subjects/FreeSurfer_analysis/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... Killed Linux salvatore-HP-630-Notebook-PC 3.19.0-33-generic #38~14.04.1-Ubuntu SMP Fri Nov 6 18:17:28 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FreeSurfer_analysis exited with ERRORS at gio 26 nov 2015, 12.42.40, CET Could you please help me to fix this problem? I tried to ran it again in an other terminal, without succeding...Thank you Best, Salvatore _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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error in mri_glmfit-sim using a per-vertex regressor
by Carme Uribe Codesal 30 Nov '15

30 Nov '15

Dear FreeSurfer users, I am trying to add a per-vertex regressor in my general lineal model (a cortical thickness analysis with the white matter-grey matter contrast parameter as regressor). I have no problems with the command line mri_glmfit: mri_glmfit --y rh.cth_corr_MMSE.mgh --fsgd cth_corr_MMSE.fsgd dods --C PDcorr.mtx --pvr rh.wgc_corr_MMSE.mgh --surf fsaverage rh --cortex --glmdir rh.cth_corr_MMSE.glmdir But when I try to run mri_glmfit-sim I think it doesn't consider the regressor (mri_glmfit-sim --glmdir lh.cth_corr_MMSE.glmdir/ --cache 1.3 abs) because I get this warning: *WARNING: unrecognized mri_glmfit cmd option --pvr* *WARNING: unrecognized mri_glmfit cmd option rh.wgc_corr_MMSE.mgh* How can I run the simulation with the regressor? Thank you very much for your help, Carme

2 1

recon-all with more than 10 inputs
by 董昊铭 30 Nov '15

30 Nov '15

Dear freesurfer exports, I am trying to recon more than 10 T1 scans from a single subject, but something went wrong. I have converted all T1 nifti files into mgz format into mri/orig directory with following names: 001.mgz 002.mgz ��. 010.mgz 011.mgz�� But when I run the command: ��recon-all �Cs ${subjec} �Cautorecon1 �Cnotal�Ccheck �Cclean-bm �Cgcut �C no-isrunning -noappend��, it seems that recon-all only recognizes the files with names 01*.mgz(i.e. 0013.mgz), the 00*.mgz(i.e. 001.mgz) files failed to be processed. Once I change the files name to ��001.mgz 002.mgz ��. 0010.mgz 0011.mgz��, the 00*. mgz(i.e. 001.mgz) are able to be recognized, but the 001*.mgz(i.e. 0013.mgz) files failed. How should I deal with this to make all files recognized? Sincerely, Dong Haoming

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