Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

White matter and cp edits don't produce new results after reconall
by Annelinde Vandenbroucke 02 Dec '15

02 Dec '15

Dear all, I have a faulty wm map (brainmask.mgz) where some regions are not labeled as white matter where they should. I tried to correct both the wm.mgz map and add control points (and saved these), afterwards running either -autorecon2-wm or autorecon2-cp, but neither of these work. I can see the control points and wm edits in my maps, but the wm segmentation is still the same. I have not found a solution on the mailing list yet and was wondering whether anybody had a similar problem or could help. Thank you in advance, Annelinde -- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720

2 9

Freesurfer Regions
by Ananth Narayanan 02 Dec '15

02 Dec '15

Hello freesurfer users, I am a new user of freesurfer. We are using FS to define ROIs for out PET analysis. I looked at the FS color lookup table, and saw the following ROIs. 8001 Thalamus-Anterior 74 130 181 0 8002 Thalamus-Ventral-anterior 242 241 240 0 8003 Thalamus-Lateral-dorsal 206 65 78 0 8004 Thalamus-Lateral-posterior 120 21 133 0 8005 Thalamus-Ventral-lateral 195 61 246 0 8006 Thalamus-Ventral-posterior-medial 3 147 6 0 8007 Thalamus-Ventral-posterior-lateral 220 251 163 0 8008 Thalamus-intralaminar 232 146 33 0 8009 Thalamus-centromedian 4 114 14 0 8010 Thalamus-mediodorsal 121 184 220 0 8011 Thalamus-medial 235 11 175 0 8012 Thalamus-pulvinar 12 46 250 0 8013 Thalamus-lateral-geniculate 203 182 143 0 8014 Thalamus-medial-geniculate 42 204 167 0 Where can I find these regions? 9000 ctx-lh-prefrontal 30 5 30 0 9001 ctx-lh-primary-motor 30 100 45 0 9002 ctx-lh-premotor 130 100 165 0 9003 ctx-lh-temporal 105 25 5 0 9004 ctx-lh-posterior-parietal 125 70 55 0 9005 ctx-lh-prim-sec-somatosensory 225 20 105 0 9006 ctx-lh-occipital 225 20 15 0 9500 ctx-rh-prefrontal 30 55 30 0 9501 ctx-rh-primary-motor 30 150 45 0 9502 ctx-rh-premotor 130 150 165 0 9503 ctx-rh-temporal 105 75 5 0 9504 ctx-rh-posterior-parietal 125 120 55 0 9505 ctx-rh-prim-sec-somatosensory 225 70 105 0 9506 ctx-rh-occipital 225 70 15 0 Also, where can I find functionally defined regions of interest? I noticed the above in the FS lookup table as well. Like the dlPFC (bilateral) and the SM1 regions of interest? But again, I can't find it. Thank you. 'Sincerely, - Ananth

2 1

problems on matrix design
by nellie 02 Dec '15

02 Dec '15

Hi Freesurfer Experts,I have tried to alter wiki example FSGD table into my analyses these days, according to your advice, but there are still some problems. Supposed there are 6 groups (maleclass1, maleclass2, maleclass3, femaleclass1, femaleclass2, femaleclass3) and 2 Variables (age, education) in my study, I have already known that:male.class1-vs-class2.mtx 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0female. class1-vs-class3.mtx 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0but I am not sure whether it is right for:male-female.mtx [1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0]/3 (Null Hypothesis: is there a difference between Males and Females regressing out the effects of class, age, and education?)class1-class2.mtx [1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 ]/2 (Null Hypothesis: is there a difference between class1 and class2 regressing out the effects of gender, age, and education?)class.diff.mtx +0.5 -0.5 0 +0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.5 0 -0.5 +0.5 0 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 (Null Hypothesis: is there a difference between class1, class2 and class3 regressing out the effects of gender, age, and educatio?)gender-x-class.mtx |+1 -1 0 -1 +1 0 0 0 0 0 0 0 0 0 0 0 0 0 | |+1 0 -1 -1 0 +1 0 0 0 0 0 0 0 0 0 0 0 0 |/2 (Null Hypothesis: is there an interaction between gender and class regressing out the effects of age and education?)gender-x-class-x-age.mtx |0 0 0 0 0 0 +1 -1 0 -1 +1 0 0 0 0 0 0 0 | |0 0 0 0 0 0 +1 0 -1 -1 0 +1 0 0 0 0 0 0 |/2 (Null Hypothesis: is there an interaction between gender, class and age regressing out the effect of education?)gender-x-class-x-age-x-education.mtx |0 0 0 0 0 0 +1 -1 0 -1 +1 0 0 0 0 0 0 0 | |0 0 0 0 0 0 +1 0 -1 -1 0 +1 0 0 0 0 0 0 |/2 |0 0 0 0 0 0 0 0 0 0 0 0 +1 -1 0 -1 +1 0 | |0 0 0 0 0 0 0 0 0 0 0 0 +1 0 -1 -1 0 +1 |/2 (Null Hypothesis: is there an interaction between gender, class, age and education?)Truly need your advice. Thanks a lot !Best,Li

1 0

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

01 Dec '15

Dear experts: In examining QDEC results of a contrast of interest, I 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. Thank you in advance. Karl

2 1

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. >

2 1

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

1 0

'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

1 0

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*

1 0

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>

2 1

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 > >

3 3

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer