Freesurfer October 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
170 discussions

Re: [Freesurfer] Quantifying volumes
by Damien MARIE 17 Oct '16

17 Oct '16

Hi, Just adding a word about the e-mail of ma colleague Josue. What he meant is that he extracted volumes for exactly the same ROI (a merging of destrieux labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using 1- a .curv file of this ROI, mri_binarize and mri_segstats or 2- a .label file of this ROI and mris_anatomical_stats. We get a different volume output (ratio of difference between the 2 methods = approx. 2.5, similar to mean thickness I would say…), so we would like to understand what is happening exactly. Using the method 1, it’s actually a surface measurement we get no? Would that be possible to convert a .cuvr file to a .label file ? Thank you and best, Damien Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700 Dear Doug, Thank you very much for your advice! We get to extract results for the volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats ), but unfortunately the results are much smaller (around 3 times) than when we extract total gray matter volumes from a respective ".label file encoded ROI" using mris_anatomical_stats . Example: Volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats): Subject1 = 1090 Subject2 = 1181 Subject3 = 713 Subject4 = 1230 Volumes from a respective ".label file encoded ROI" (mris_anatomical_stats): Subject1 = 3497 Subject2 = 3786 Subject3 = 2268 Subject4 = 3491 Are the volumes extracted from a ".curv file encoded ROI" (using mri_binarize and mri_segstats) an estimation of the total gray matter volumes? Why these values are differing that much? Thank you very much, Josue Dalboni ________________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...(a)nmr.mgh.harvard.edu> Sent: Wednesday, October 5, 2016 5:19 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes I would binarize the curv file with mri_binarize --i lh.yourcurvfile --abs --min .0000001 --o lh.yourcurvfilebin.mgh Then compute the volume with mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume --accumulate --sum lh.vol.yourcurv.sum On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote: > Dear Douglas, > > I have a ".curv" file that contains the curvature information inside an > automatically delineated ROI and 0 everywhere else. > I would like to calculate the volume of this ROI, > > Can I extract statistics directly from the ".curv" file? > > Best regards, > Josue > ________________________________________ > From: freesurfer-boun...(a)nmr.mgh.harvard.edu > <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...(a)nmr.mgh.harvard.edu> > Sent: Tuesday, October 4, 2016 9:41 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Quantifying volumes > > What is the nature of the segmentation? Is it just a binary (1=in, > 0=out) segmentation? And what file format? In general we don't use .w > anymore, but it can be converted into something else. > > doug > > > On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote: >> Dear Douglas, >> >> >> I have a segmented gyrus curvature file (.curv or .w) and I would like >> to calculate the volume (and other statistics) of this gyrus. >> >> >> I currently only know mris_anatomical_stats to perform that, but >> requiring a '.label' file. >> >> >> Can I extract statistics directly from the ".curv" file? >> >> >> Or can I convert directly from .curv to .label in order to extract >> these statistics? >> >> >> As another option, is it feasible to convert the '.curv' file to nifti >> volume (mri_surf2vol), binarize it (mri_binarize), and then convert to >> label (mri_cor2label)? >> >> >> What does the output nifti file from 'mri_surf2vol' contain? Does it >> contain the complete volume behind the surface? Or does it only >> contain the surface over the 3D space? >> >> >> Thank you very much in advance for your help! >> >> >> Best regards, >> >> Josue >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Job offer: research-fellow position in Japan
by Jarek Rokicki 17 Oct '16

17 Oct '16

A research-fellow post is available at the Integrative Brain Imaging Center, National Center of Neurology and Psychiatry. We are looking for a candidate with expertise in MRI, fMRI, PET (optional) image analysis and with a strong publication record. You are expected to take a lead or co-author role in publishing existing datasets within the lab, as well as acquiring new data, data analysis and novel algorithm development. *Your responsibilities will include:* 1. Analysis of behavioral and neuroimaging data 2. Presentations at national and international meetings 3. Manuscript preparation for publication *Required skills:* 1. A doctoral degree and publication record in cognitive science, neuroscience, computer science or related field 2. An independent, target-driven attitude 3. Matlab or Python or C++ programming skills 4. Familiarity with Unix based operating systems 5. At least 3 month experience of living abroad 6. Basic background in statistics 7. Experience with FSL, or SPM, or conn, or AFNI, R, SPSS 8. Fluency in English – written and oral 9. Japanese is not necessary, but beneficial *About the post:* 1. One year contract, extensible up to 3 years 2. Salary is based on a per hour basis: 1 hour = from 1840 to 2652 yen depending on experience and qualifications (in case of medical license holder 2800 yen). Additionally, travel allowance and other bonuses are offered. 3. Working hours: up to 31 hours/week (+ up to 200 hours of paid overtime/year) 4. Social insurance, unemployment insurance, accident insurance are covered by the Center 5. A dorm room is available for singles *To apply, please send the following documents:* 1. CV (with picture) 2. List of publications and international conferences attended 3. Summary of major research achievements and future research objectives (up to 400 words) 4. Reference from your direct supervisor or your current workplace (reference should be addressed to the President of National Center of Neurology and Psychiatry) For more details on the Center, please go to: http://www.ncnp.go.jp/ibic/ english/index.html Interested parties should email all necessary papers to matsudah(a)ncnp.go.jp <matsudah(a)ncno.go.jp> 宜しくお願い致します。 Sincerely, Jarek Rokicki, Ph.D. Integrative Brain Imaging Center (IBIC) National Center of Neurology and Psychiatry (NCNP) *4-1-1 Ogawahigashi-chyo, Kodaira, Tokyo 187-8551 Japan* TEL: +81-80-6628-5709 国立精神・神経医療研究センター脳病態統合イメージングセンター(IBIC) 臨床脳画像研究部画像情報解析研究室 *〒187-8551 東京都小平市小川東町4-1-1*

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Volume or surface?
by John Anderson 17 Oct '16

17 Oct '16

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FreeSurfer on MP2RAGE
by Daniel Ferreira 16 Oct '16

16 Oct '16

Dear all, We have been working quite extensively with Freesurfer over the years. We are now starting to collect a new large cohort and we are about to decide which T1-weighted sequence to use, MPRAGE or MP2RAGE (Siemens 3T Prisma, headcoil 20 Chanel). When we visually inspect the images we think there is a better contrast between GM and WM in the MP2RAGE over the traditional MPRAGE sequence. Both sequences seem to produce good Freesurfer output, but the cortex tend to be a bit thinner with MP2RAGE, possibly due to the better contrast, but we can of course not be sure of this. Freesurfer have always produced nice results with the MPRAGE sequence and the MPRAGE flag seems to work well. Do you think this flag will work as well on MP2RAGE? Of course it is difficult to say but we wonder if you have any opinion on which sequence to use? Thank you very much, Best regards -- Daniel Ferreira, PhD. Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics (Karolinska Institute, Sweden) daniferp(a)gmail.com | daniel.ferreira.padilla(a)ki.se

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Re: [Freesurfer] Freesurfer Digest, Vol 152, Issue 22
by AKUDJEDU, THEOPHILUS 16 Oct '16

16 Oct '16

Dear All, I want to know the freesurfer anatomical definition for the caudate and the hippocampus. Thank you. Theo ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: 16 October 2016 17:00:01 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 152, Issue 22 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. Using "for" to run multiple subjects (Farzaneh keyvanfard) 2. Problem in upload file through ftp (Cong) ---------------------------------------------------------------------- Message: 1 Date: Sat, 15 Oct 2016 18:52:12 +0000 (UTC) From: Farzaneh keyvanfard <f_keivanfard(a)yahoo.com> Subject: [Freesurfer] Using "for" to run multiple subjects To: Freesurfer Support List <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <941247766.328043.1476557532300(a)mail.yahoo.com> Content-Type: text/plain; charset="utf-8" Dear expert, I want to run recon-all for 100 subject simultaneously. I found the following link about it, but as I'm a beginner in this field, I don't understand how to use it. Would you please kindly give an example with a subject names, directory , etc. what should be written instead of * , or how could I define the number of subjects, ...? Thank you very much. https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/Two Best Regards F.Keyvanfard

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Problem in upload file through ftp
by Cong 16 Oct '16

16 Oct '16

Dear freesurfer experts When I use command "put path/to/my/file”, it’s always appear an error "229 Entering Extended Passive Mode (|||37867|). 553 Could not create file”, if I use epsv command before put, then comes an error "227 Entering Passive Mode (132,183,202,158,147,237). 553 Could not create file”. Could you give me some advices? Best Wishes Cong Chen

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group analysis
by charles laidi 14 Oct '16

14 Oct '16

Dear FreeSurfers, I would like to study the interaction between age and cortical thickness in patients and controls. My hypothesis is that there is an interaction and that cortical thickness is decreasing faster with age in patients than in controls. I have both Male and Female included in 6 different centers. I would like to consider also Gender and Site (6 centers) as confounds. My understanding is that I should perform a surface based group analysis with freesurfer. I am not able to find an example for my problem in the documentation https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V Would anyone had some tips to build the Fsgd file and the contrast file ? Thank you very much in advance. Best, Charles

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MRI_segstats for adc.nii from dt recon - increasing decimal digits
by Chung, Yoonho 14 Oct '16

14 Oct '16

Hi! I ran mri_segstats as instructed in the wiki to extract ADC values from adc.nii. And as you can see below in my output, I think the decimal digits are truncated and missing the following decimal values. Is there an option or other way to get around this problem and extract ADC values from the ROIS with greater precision? Thank you! mri_segstats \ --seg $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --id 251 --id 3021 --id 3024 --id 3030 --id 12 --id 4 \ --i adc.nii --sum adc.stat # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 29 3001 344 2752.0 wm-lh-bankssts 0.0007 0.0001 0.0006 0.0009 0.0003 30 3002 450 3600.0 wm-lh-caudalanteriorcingulate 0.0009 0.0003 0.0006 0.0026 0.0020 31 3003 851 6808.0 wm-lh-caudalmiddlefrontal 0.0007 0.0001 0.0005 0.0010 0.0005 32 3005 337 2696.0 wm-lh-cuneus 0.0008 0.0001 0.0006 0.0011 0.0005 33 3006 82 656.0 wm-lh-entorhinal 0.0009 0.0001 0.0008 0.0016 0.0008

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No cluster remains significant after multiple comparisons
by Karamfil Bahchevanov 14 Oct '16

14 Oct '16

Hello Freesurfer experts, I'm really struggling with my study. I have a 27 scans that I analyze in QDEC. Scans are from Siemens machine, mprage protocol, TR1620, TE 4.3, FOV 240*256, acq. matrix 232*256, slice thickness 0,9mm. After I enter model and have some initial significant clusters (threshold 2 - 5) I run multiple comparisons, and none have survived the procedures, no matter method or significance - FDR (0.1-0.05-0.01) or Monte-Carlo(0.05-0.01-0.01). This repeats no matter of the tested variables and the initial significancy and size of the clusters. I'm really confused of that and could not find an explanation, except that my study is really non-significant. However, the significant results I get are in the regions that I expect to be, that are reported previously and they also explain my results. If they happen to survive, but that never is the case (In fact one survived, but I entered wrong variables and model was wrong). What could be the reason? Outliers? Really non-significant results (which I doubt as I said already)? Should I recheck the quality of the processed scans? I also made my own average, hoping to improve things somehow, but QDEC doesn't allow me to run multiple comparisons with it. Anyway, is it mistake to discuss the results when they don't survive simulation, as they fit with initial hipothesis and what I'm testing. I have to point that there are only few significant clusters, that could not be explained with what I'm testing and tested population, so in fact the "noise" is very small. Any help will be of great value, Thanks

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Warping an ROI from one subject to another
by Joel Bruss 14 Oct '16

14 Oct '16

I have two subjects, subA and subB. subA has a binary ROI mask, native space, that I'd like to place in subB's native space. Both subjects have been run through all stages of recon, edited, etc. Is there a better or easier way to achieve this than what I've run?: #Resample the native space binary ROI file into "brainmask" space mri_convert -rl /subA/mri/brainmask.mgz -rt nearest --no_scale 1 ROI.nii.gz /subA/mri/ROI.mgz #Convert ROI file into a label mri_cor2label --id 1 --c /subA/mri --i ROI.mgz --l ROI.label #Move label from subA to subB mri_label2label --srcsubject subA --srclabel /subA/mri/ROI.label --trgsubject subB --trglabel /subB/mri/ROI_to_subB.label --regmethod volume #Convert warped ROI label to a volume mri_label2vol --label /subB/mri/ROI_to_subB.label \ --subject subB \ --temp brainmask.mgz \ --regheader brainmask.mgz \ --o /subB/mri/ROI_to_subB.mgz #Convert the volume back to native subB space mri_convert -rl subB_native.nii.gz -rt nearest --no_scale 1 /subB/mri/ROI_to_subB.mgz ROI_to_subB_native.nii.gz A few follow-up questions: 1) When running mri_label2label, is better to use surface or volume for the "regmethod"? Which method will give me a better fit for my output? 2) The output I'm getting looks striped (there are holes in the binary mask) and doesn't quite fit the anatomy (the final file is shifted up and away from where I would expect it to be although in the general vicinity of what I would expect). It's almost as if I've chosen a wrong target or file along the way. I don't expect the fit to be perfect, but did I do something wrong? Thanks in advance to any and all replies. ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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Freesurfer October 2016