Freesurfer

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16 participants
30084 discussions

nu_correct error (FS 6 beta)
by COX Simon 03 Dec '15

03 Dec '15

Dear all, I'd be very grateful for a bit of help with the following problem. I'm running FreeSurfer 6.0 (I read a suggestion that there had been some compatibility issues running the current stable FS release with newer versions of openSUSE) on a cluster. However, nu_correct seems to be hitting an issue: ncopen: filename "./tmp.mri_nu_correct.mni.9548/0/nu1_est.mnc.temp": No such file or directory miopen: MINC package entry point nu_estimate_np_and_em: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct The directory exists, and there are several other files written here ("nu0.mnc", "nu1_corr.mnc", "nu1_mask.mnc", "nu1_residue.mnc" and "nu1_temp.mnc") so it doesn't appear to be having an issue with write access to this location. Many thanks in advance for your help, Simon ____ Simon R. Cox Centre for Cognitive Ageing and Cognitive Epidemiology University of Edinburgh 7 George Square Edinburgh EH8 9JZ The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image
by Ajay Kurani 03 Dec '15

03 Dec '15

Hello Freesurfer experts, I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version) with the -hires flag to process an MNI template image which is 0.5mm isotropic. Stage 1 ran well and on stage 2 there is an error during pocessing: Command run: recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts I supplied a skull stripped brain which was nu corrected and so I used the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 stage. I then ran autorecon2 and it was working well until I was at the -fix stage and ran into the following error: Error: mris_euler_number ./surf/lh.orig mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list I am not sure if this is due to the fact that we have a very high resolution image (template) and if there are any modifications needed aside from the hires flag. Are there any suggestions you have? Thanks, Ajay

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Freesurfer Version mismatch between Subject and Control Stamp in autorecon2 and autorecon3
by Amy L 03 Dec '15

03 Dec '15

Hi all, I'm sorry if this is a silly question, but what might cause the version of Freesurfer to be different in the Subject and Current Stamps of the output following autorecon2 and autorecon3? And is this a problem? The relevant lines of output are as follows: INFO: FreeSurfer build stamps do not matchSubject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Thanks very much for any insight!

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Re: [Freesurfer] Error - extracting percent signal
by Danielle Miller 02 Dec '15

02 Dec '15

Sure -- should be all here now! The last email contained the following text: "Hi Doug, > > Thanks for the response. I used the mri_label2label command: > mri_label2label --srclabel <labelfile> --s fsaverage --regmethod vol > --paint dmax --trglabel <output> --hemi lh > > When I input the output from this into mri_segstats as the --seg > volume, I get the error: > mri_read(): couldn't determine type of file > fsaverage/label/lh_ACC_label_test.label > ERROR loading fsaverage/label/lh_ACC_label_test.label > > Is there another step I am missing?" 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 Hi Danielle, can you resubmit this email with the previous correspondence? On 12/02/2015 01:14 PM, Danielle Miller wrote: > Hi Doug, > > Thanks for the response. I used the mri_label2label command: > mri_label2label --srclabel <labelfile> --s fsaverage --regmethod vol > --paint dmax --trglabel <output> --hemi lh > > When I input the output from this into mri_segstats as the --seg > volume, I get the error: > mri_read(): couldn't determine type of file > fsaverage/label/lh_ACC_label_test.label > ERROR loading fsaverage/label/lh_ACC_label_test.label > > Is there another step I am missing? > > -- > 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 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

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Re: [Freesurfer] Error - extracting percent signal
by Danielle Miller 02 Dec '15

02 Dec '15

Hi Doug, Thanks for the response. I used the mri_label2label command: mri_label2label --srclabel <labelfile> --s fsaverage --regmethod vol --paint dmax --trglabel <output> --hemi lh When I input the output from this into mri_segstats as the --seg volume, I get the error: mri_read(): couldn't determine type of file fsaverage/label/lh_ACC_label_test.label ERROR loading fsaverage/label/lh_ACC_label_test.label Is there another step I am missing? -- 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

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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

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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

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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

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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

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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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