Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation
by Gabor Perlaki 23 Jan '18

23 Jan '18

Dear Iglesias, Do you think that it is useful to also use a fieldmap for hippocampal subfield segmentation? Can Freesurfer's hippocampal subfield segmentation use it? I'm not sure that due to the limited resolution of the fieldmap and due to registration issues it is worth to acquire a fieldmap for hippocampal subfield segmentation. What do you think? Best, Gabor

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Inquiry about process time by use "recon-all"
by Ritthikrai Thaweecharoen 23 Jan '18

23 Jan '18

Dear FreeSurfer Staff, We have conducted a brain volume study in normal Thai elderly. We found that the process time to analyze the brain of 20% of our subject took over 40 hours. The maximum process time is 99 hours. Eventhough the size of imaging file is around 20 MB and use “recon -all” command to process file. It would be grateful if you could help to explain tedious process time of FreeSurfer and how to shorten this process time. Our Machine spec. is as following: • INTEL i5 – 4260U CPU(a)1.4GHz • RAM 8 MB • Cent OS 6.x Best Regards Ritthikrai Thaweecharoen Data Scientist Research and Development Department Tel: 02 755 1919 Email Disclaimer : The information contained in this electronic mail message may be confidential and protected information intended only for the use of the entity name above. As the recipient of this information you may be prohibited by law from disclosing this information to any other parties without specific written authorization from the individual to whom it pertains. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any disclosure, dissemination, distribution, copying, or action taken in reliance on the contents of this communication is strictly prohibited, If you have received this communication in error, please notify me back immediately by telephone and destroy the message and its attachments.

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freesurfer bids app cannot find license file
by Dianne Patterson 22 Jan '18

22 Jan '18

After trying the example bids app (which worked fine), I am trying the freesurfer bids app: https://github.com/BIDS-Apps/freesurfer I have built the docker container on my mac and I have the ds005 data directory here and the license.txt which I requested from freesurfer. I asked for a linux license (assuming the container contains linux and that was the relevant fact). dpat@Saci:/Volumes/Main/Working/BIDS_TESTING% docker run -ti --rm -v /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer /bids_dataset /outputs participant --license_file "license.txt" 1: You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. (code: 13 - SLICE_TIMING_NOT_DEFINED) /sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz /sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz /sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz /sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz /sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz /sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz /sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz /sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz /sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz /sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz ... and 38 more files having this issue (Use --verbose to see them all). Summary: Available Tasks: Available Modalities: 133 Files, 1.77GB mixed-gambles task T1w 16 - Subjects inplaneT2 1 - Session bold Traceback (most recent call last): File "/run.py", line 165, in <module> raise Exception("Provided license file does not exist") *Exception: Provided license file does not exist* =========== If I provide the full path to the license file, it still fails: docker run -ti --rm -v /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer /bids_dataset /outputs participant --license_file "/Volumes/Main/Working/BIDS_ TESTING/license.txt" Suggestions? How do I tell freesurfer where the license file is? Thanks so much, Dianne -- Dianne Patterson, Ph.D. Research Scientist dkp(a)email.arizona.edu <dkp(a)u.arizona.edu> or diannepat(a)gmail.com University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) ============== If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account. ============== Antipiphany: That moment when you realize how little you actually know ============== -- Dianne Patterson, Ph.D. Research Scientist dkp(a)email.arizona.edu <dkp(a)u.arizona.edu> or diannepat(a)gmail.com University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) ============== If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account. ============== Antipiphany: That moment when you realize how little you actually know ==============

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Re: [Freesurfer] TRACULA QC
by Yendiki, Anastasia 22 Jan '18

22 Jan '18

Hi Linnea – Before the stats are computed, the probability distribution of the paths is thresholded to 20% of its peak value, so voxels with very low probability will not affect the outcome. Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Linnea Marie Dramdal Borg <lmborg(a)stud.ntnu.no<mailto:lmborg@stud.ntnu.no>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, January 22, 2018 at 10:26 AM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] TRACULA QC Hi, We have run into some issues with our tractographies. I have attached examples: In "fmajor_4053.png", there is a "bridge" in forceps minor on its way to the frontal lobe. We've also come across other cases of bridging in forceps minor, such as "fminor_4013". Also, there are some voxel paths that are rather weak, such as "unc_2068_1.png" and "unc_3022_1.png"/"unc_3022_2.png". This does not seem optimal. Do you agree? We've also come across a couple of cases where it hasn't really found the tract correctly, such as in "29_ccg_1", "unc_3045_1.png" and "268_ccg.png". This also includes "fmm_32.png", which has a nice voxel intensity, but neither the forceps minor nor major voxels really fit their underlying tracts. Finally, neither "unc_3068_2.png" nor "unc_4040.png" are really correct. Should we reinitialize all of them, or can we use some of them without affecting the results too much? Thank you, Linnea Marie

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FreeSurfer Installation
by Caio Quini 22 Jan '18

22 Jan '18

Hello I am trying to download FreeSurfer from freesurfer.net and I can't open the download page. It keeps returning an error message. Is that a common error? Is there any other way to download the software? Thank you very much. Regards Caio Quini

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Anatomical ROI analysis
by Ting Li 22 Jan '18

22 Jan '18

Hi, all experts, I am studying the AnatomicalROIV6.0 tutorials. In the Anatomical ROI analysis tutorial, the first four part work well. While in the Group stats files, I got an error information like this. group_analysis_tutorial ting$ asegstats2table --subjects 004 021 040 067 080 092 \ > --segno 11 17 18 \ > --tablefile aseg.vol.table File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax Thanks for your help. Ting

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recon-all error
by "Julia Ströhlein" 22 Jan '18

22 Jan '18

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Hippocampal subfields segmentation
by Alexis Guyot 22 Jan '18

22 Jan '18

Dear Freesurfer developers, I have been trying to segment (with Freesurfer v6.0.0, on Ubuntu 14.04) the hippocampal subfields of two 7T MR images in NIFTI format: an isotropic (0.8*0.8*0.8 mm3) whole-brain T1-weighted source volume with an anisotropic (0.3*1.2*0.3 mm3) T2-weighted volume covering the brain partially and centred on a region comprising both hippocampi. I have followed the instructions in https://surfer.nmr.mgh. harvard.edu/fswiki/HighFieldRecon to correct the bias in the two 7T volumes ('T1_biasCorrected.png', 'T2_biasCorrected.png'). I have run 'recon-all -hires [...] -expert expert.txt' ('expert.txt') on my bias-corrected T1 volume, which produced an accurate segmentation ('aseg.png', 'recon-all.log'). Following this, I have run 'recon-all -hippocampal-subfields-T2' on the bias-corrected T2 volume ('hippocampal-subfields-T2.log'). Looking at the resulting segmentation, I am unsure the molecular layer has been properly delineated in the body of the hippocampus ('right_hippocampus_body.png', 'right_hippocampus_body_seg.png'). In addition, it appears the convolutions in the hippocampal head have not been correctly segmented ('right_hippocampus_head.png', 'right_hippocampus_head_seg.png'). I am not certain this is the expected behaviour when running the hippocampal subfields module on high-res data. Is it possible the recon-all output is not accurate enough (should I adjust the mres_inflate value prior to segmenting the brain)? Could the high anisotropy of the T2 volume hinder the segmentation process? Any thoughts on this? Screenshots/attachments are available on request, as my previous message was rejected for being too big. Thanks for your help, Alexis

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Re: [Freesurfer] [Re] medial wall label in Freesurfer 6
by M del Mar Velasco 22 Jan '18

22 Jan '18

Hi Andrew, My test in December with last version of make_average_surface worked correctly. However, now I am trying to make another average subject and medial_wall.label is not created. I am using the last patch as last time. It is unusual because last time label folder was correctly created. I have realized mri_aparc2aseg is not working fine because I get an error log. I've attached it. I can send you to our ftp server whole average subject folder if you consider it appropiate. Many thanks, Cheers, M del Mar

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Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?
by Michelle VanTieghem 22 Jan '18

22 Jan '18

Hi, I went ahead and re-processed all of our data with the newest version (6.0) of freesurfer (I didn't hear back from anyone on this issue for over a month). It does make a significant difference for our dataset. Pial mater is no longer labeled as gray matter with version 6, which was a significant issue for the majority of our images when using version 5.3. I've attached screen shot examples her (v5.3 on right, v6 on left). I thought this would be useful for other users to know! Thanks, Michelle On Tue, Jan 2, 2018 at 9:36 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Michelle > > if you point me at a dataset (an entire subject dir gzipped and uploaded > to our ftp site) and some voxel coordinates of where you see problems, I'll > take a look. > > cheers > Bruce > > > > On Fri, 22 Dec 2017, Michelle VanTieghem wrote: > > >> Hi Douglas, >> >> I have reported many problems with the skull stripping and resulting >> issues in freesurfer. to >> summarize: >> >> 1. For our structural scans, we have significant pial matter/dura matter >> remaining for about 50% of >> subjects or more (of a dataset of 350 scans). I have tested using >> freesurfer's gcut and other >> options, as well as AFNI skull strip, FSL with many options, and even >> ANTS. >> >> 2. We gave up on trying to use surfaces with this dataset, due to the >> sheer amount of manual >> intervention that would be needed to edit the brains >> >> 3. The aseg almost always labels the remaining skull as gray matter, >> which then influences the icv >> and wbv measurements. W >> >> 4. Recently we have decided to try the longitudinal pipeline. Another >> problem appears: if a >> cross-sectional scan does not have any pial matter (as in, it is one of >> the few that as successfully >> skull stripped - we call these the "clean" scans) but a template is made >> from multiple scans from >> this subject. If one of those other tp scans from this subject has any >> pial mater remaining, then >> the (a) the template will include all of the pial matter and (b) the >> longitudinal version of the >> "clean" scan now has extra pial matter that gets erroneously labeled as >> gray matter, or sometimes >> white matter. Attached is a screenshot example of this problem. >> >> I have been trying to solve this for over a year, and I also sent data to >> freesurfer over the ftp on >> December 1st using the directions on the freesurfer wiki, if you want to >> take a look at a single >> representative scan with this skull strip issue. >> >> Thanks! >> >> Michelle >> >> >> ---- >> >> Douglas N Greve Tue, 19 Dec 2017 15:25:14 -0800 >> >> Hi Michelle, sorry about not getting to this before. It looks like Bruce >> was helping you out, but he's just left and won't be back until the new >> year. To answer your first question, I don't think that v6 performs much >> differently on skull stripping than v5.3. What is the nature of the skull >> stripping problem? Can you send screen shots? >> >> doug >> >> >> On Tue, Dec 19, 2017 at 3:47 PM, Michelle VanTieghem < >> michelle.vantieghem(a)gmail.com> wrote: >> Hi, >> I am following up again -- on my prior posts regarding skull strip >> issues and whether >> using freesurfer 6.0 would improve over freesurfer 5.3 . >> I sent the data over the ftp on Dec 1 and would greatly appreciate it if >> you could take a >> look to see if there is a way to improve the skull strip since we have >> this issue with 100+ >> scans and my attempts to use gcut, and other skullstrip programs, has not >> worked. >> >> Thank you, >> Michelle >> >> On Fri, Dec 8, 2017 at 12:31 PM, Michelle VanTieghem < >> michelle.vantieghem(a)gmail.com> wrote: >> Hi, >> I am just following up on my prior posts regarding skull strip issues and >> whether using >> freesurfer 6.0 would improve over freesurfer 5.3 . >> I sent the data over the ftp and would greatly appreciate it if you could >> take a look to >> see if there is a way to improve the skull strip since we have this issue >> with 100+ >> scans and my attempts to use gcut, and other skullstrip programs, has not >> worked. >> >> Thank you, >> Michelle >> >> On Fri, Dec 1, 2017 at 5:08 PM, Michelle VanTieghem < >> michelle.vantieghem(a)gmail.com> >> wrote: >> Ok that worked. I sent the data for a subject with the skull >> stripping issue >> that is common in most of our dataset. >> Thanks, >> Michelle >> >> On Fri, Dec 1, 2017 at 4:56 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> try cd'ing to incoming not outgoing (the names are from our >> perspective I think :) >> >> On Fri, 1 Dec 2017, Michelle VanTieghem wrote: >> >> >> yn-128-59-230-36:structural michellevantieghem2$ ftp >> surfer.nmr.mgh.harvard.edu >> >> Connected to surfer.nmr.mgh.harvard.edu. >> >> 220-This is the Martinos Center Anonymous FTP service. Use >> of this site >> >> 220-shows implicit consent to our Acceptable Use Policy >> outlined at >> >> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/compute >> r/nmr-aup.php >> >> >> 220- >> >> 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you >> encounter either >> >> 220- >> >> 220-229 Entering Extended Passive Mode >> >> 220- >> >> 220- and nothing happens OR >> >> 220- >> >> 220-229 Entering Extended Passive Mode >> >> 220-500 Bad EPRT protocol. >> >> 220- >> >> 220- try issuing the EPSV command prior >> to GET or PUT. >> >> 220- >> >> 220 >> >> Name (surfer.nmr.mgh.harvard.edu:michellevantieghem2): >> anonymous >> >> 331 Please specify the password. >> >> Password: >> >> 230 Login successful. >> >> Remote system type is UNIX. >> >> Using binary mode to transfer files. >> >> ftp> cd transfer/outgoing >> >> 250 Directory successfully changed. >> >> ftp> put SB152_freesurfer.tar.gz >> >> local: SB152_freesurfer.tar.gz remote: >> SB152_freesurfer.tar.gz >> >> 229 Entering Extended Passive Mode (|||37860|). >> >> 553 Could not create file. >> >> ftp> ls >> >> 229 Entering Extended Passive Mode (|||37896|). >> >> 150 Here comes the directory listing. >> >> -rw-r--r-- 1 0 0 3812 Dec 01 06:10 >> README.1st >> >> drwxrwsr-t 4 0 1046 4096 Nov 21 2014 >> flat >> >> drwxrwsr-t 13 0 160 4096 Aug 19 2013 >> fsdev >> >> drwxrwsr-t 14 0 1046 4096 Dec 05 2011 >> recon >> >> drwxrwsr-t 3 0 18 4096 Jan 24 2005 >> sysadm >> >> 226 Directory send OK. >> >> ftp> ls >> >> 229 Entering Extended Passive Mode (|||37892|). >> >> 150 Here comes the directory listing. >> >> -rw-r--r-- 1 0 0 3812 Dec 01 06:10 >> README.1st >> >> drwxrwsr-t 4 0 1046 4096 Nov 21 2014 >> flat >> >> drwxrwsr-t 13 0 160 4096 Aug 19 2013 >> fsdev >> >> drwxrwsr-t 14 0 1046 4096 Dec 05 2011 >> recon >> >> drwxrwsr-t 3 0 18 4096 Jan 24 2005 >> sysadm >> >> 226 Directory send OK. >> >> ftp> put SB152_freesurfer.tar.gz >> >> local: SB152_freesurfer.tar.gz remote: >> SB152_freesurfer.tar.gz >> >> 229 Entering Extended Passive Mode (|||37898|). >> >> 553 Could not create file. >> >> ftp> >> >> >> On Fri, Dec 1, 2017 at 4:50 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> can you paste the full session text into the email >> (not as a screen shot)? >> >> On Fri, 1 Dec 2017, Michelle VanTieghem wrote: >> >> Hi, I am unsure whether this worked: see >> attached screenshot. >> >> Thanks! >> M >> >> On Fri, Dec 1, 2017 at 4:26 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> yes, it should. You should just be able >> to do a "put" >> On Fri, 1 Dec 2017, Michelle VanTieghem >> wrote: >> >> Hi, >> I am confused by the instructions >> for the ftp. Once I am logged into the ftp and have >> navigated to >> the transfer/incoming >> directory, how am I supposed to >> find / access the file that I would ike to send >> through? Does >> terminal still recognize my >> working directory before I logged >> into the ftp? >> >> Thanks! >> Michelle >> >> On Sat, Nov 18, 2017 at 2:54 PM, >> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Michelle >> >> probably best to tar and >> gzip the entire subject directory and ftp it to us: >> >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange >> >> cheers >> Bruce >> >> On Sat, 18 Nov 2017, >> Michelle VanTieghem wrote: >> >> Hi, >> Yes I can send you the >> data - should I just attach the mprage file in the >> email, or is >> there >> another >> way to share the data >> with freesurfer? Also, should I send one scan or >> multiple >> scans? >> >> Thanks, >> Michelle >> >> On Sat, Nov 18, 2017 >> at 10:37 AM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Michelle >> >> are you doing >> anything out of the ordinary? Do you want to send us a >> dataset and >> we will >> take a look? I >> don't think 6.0 is very different from 5.3 in regard >> to skull >> stripping, >> although it is >> probably a bit better >> >> Bruce >> >> On Fri, 17 Nov >> 2017, Michelle VanTieghem wrote: >> >> Hello, >> I have >> posted several times about problems with >> skull-stripping with our >> dataset. >> We have tried gcut >> and >> multiple other options in other packages (AFNI, FSL, ANTS) >> to remove >> skull from >> structural >> images in >> our dataset with little success. >> >> Recently, >> a colleague suggested this may be due to versions: >> that 6.0 >> deals >> with skull >> stripping >> much >> better than 5.3. >> >> I wanted >> to ask if indeed this could be the case before I go >> install 6.0 >> and re-run >> everything in >> my study. >> >> Thank >> you, >> Michelle >> >> -- >> Michelle >> VanTieghem >> PhD >> student in Psychology >> >> Developmental Affective Neuroscience Lab >> Columbia >> University >> >> mrv2115(a)columbia.edu >> >> >> >> >> 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. >> >> >> >> >> -- >> Michelle VanTieghem >> PhD student in >> Psychology >> Developmental >> Affective Neuroscience Lab >> Columbia University >> mrv2115(a)columbia.edu >> >> >> >> >> -- >> Michelle VanTieghem >> PhD student in Psychology >> Developmental Affective >> Neuroscience Lab >> Columbia University >> mrv2115(a)columbia.edu >> >> >> >> >> -- >> Michelle VanTieghem >> PhD student in Psychology >> Developmental Affective Neuroscience Lab >> Columbia University >> mrv2115(a)columbia.edu >> >> >> >> >> -- >> Michelle VanTieghem >> PhD student in Psychology >> Developmental Affective Neuroscience Lab >> Columbia University >> mrv2115(a)columbia.edu >> >> >> >> >> -- >> Michelle VanTieghem >> PhD student in Psychology >> Developmental Affective Neuroscience Lab >> Columbia University >> mrv2115(a)columbia.edu >> >> >> >> >> -- >> Michelle VanTieghem >> PhD student in Psychology >> Developmental Affective Neuroscience Lab >> Columbia University >> mrv2115(a)columbia.edu >> >> >> >> >> -- >> Michelle VanTieghem >> PhD student in Psychology >> Developmental Affective Neuroscience Lab >> Columbia University >> mrv2115(a)columbia.edu >> >> >> >> >> -- >> Michelle VanTieghem >> PhD student in Psychology >> Developmental Affective Neuroscience Lab >> Columbia University >> mrv2115(a)columbia.edu >> >> -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

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Freesurfer January 2018