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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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Linear Mixed Effect Modle
by lanbo Wang 22 Jan '18

22 Jan '18

Hi, all experts. When I try to use LME model. There is a code "mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh" in LME tutorials website under *"b)Mass-univariate". * When I ran it, error happened: """ [mtobia@localhost PD]$ mris_preproc --qdec-long $SUBJECTS_DIR/sub_long.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.long.mgh nsubjects = 80 ERROR: cannot find /HD4/PD/Patients_Symptom//.long. """ And I already check the file name, The folder name match <fsid>.long.<fsid_base>. What should I do now? Thanks for your help. Best, Lanbo

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TRACULA QC
by Linnea Marie Dramdal Borg 22 Jan '18

22 Jan '18

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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convert nii to nii.gz
by Ting Li 22 Jan '18

22 Jan '18

Hi Freesurfer Expert, I am very new to Freesurfer and have a very basic question. How to convert .nii files to nii.gz? I have tried the mri_convert subject_name.nii to subject_name.nii.gz directly. It gives me an error information that mri_convert: command not found. Thanks for your help! Best, Ting

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bert log file
by Renew Andrade 21 Jan '18

21 Jan '18

Hello everyone!I write to you because I can't get the process done in freesurfer. I attach the log file. Thank you!

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dt_recon error: MatrixReadTxt: could not scan value [1][1]
by Adam Mecca 20 Jan '18

20 Jan '18

Hello FreeSurfer Developers, I'm trying to pre-process some diffusion data based on the tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0 I am getting the following warning followed by the program hanging -------------------------- Creating output directory /home1/am2359/fs6_data/fpeb_app_fs/fpeb001/dtrecon Loading y from /home1/am2359/fs6_data/fpeb_app_fs/fpeb001/dtrecon/dwi-ec.nii.gz ... done reading. MatrixReadTxT: could not scan value [1][1] WARNING: matlab elment type is 1869357167, which is not a matrix. could not allocate 543518770 x 1683973236 matrix Cannot allocate memory unsupported matlab format 1678398324 (unknown) Cannot allocate memory ---------------------------------- I would greatly appreciate your assistance. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: CentOS release 6.9 (Final) 3) uname -a: Linux ariespet.med.yale.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Mar 21 19:29:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) dt_recon.log: see attached Thank you, Adam

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corRead(): can't open file /home/andraderenew/COR-.info
by Renew Andrade 19 Jan '18

19 Jan '18

Hello: I run the command to open freeview -v…(the installation guide example in Bert) and I get the error in I point out in the subject of this email. Thanks for the help in advance! Sincerely, Rene Andrade.

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Hippocampal segmentation flips on the left side
by Tuominen, Lauri Johannes 19 Jan '18

19 Jan '18

Dear Freesurfers, When I run freesurfer 6.0 recon-all -hippocampal-subfields-T1 command to segment an MNI152 template, the resulting segmentation of left hippocampus got flipped in left-right dimension. Otherwise the right hippocampus and other subcortical segmentations in the aseg-file look fine. I encountered a similar problem when I tried to segment a T1 acquired at 7T. I run the command both locally and then on launchpad. Would you know how to fix this? Thanks so much for your advice! Lauri Tuominen

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