Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

White matter segmentation
by yusif Al-kheder 02 Mar '17

02 Mar '17

Hello, Is it possible to segment the brain into these parts if possible using freesurfer; Cerebellum Midbrain Pons Medulla Oblongata Hippocampus Thalamus Hypothalamus Anterior and Posterior Commissura Corpus Callosum Hypophysis Dura Mater Youssif

2 3

Re: [Freesurfer] mri_convert error: \'GetDICOMInfo(): dcmGetDWIParams() 7\' in FS6.0
by Douglas N Greve 02 Mar '17

02 Mar '17

When you were getting the error message, was the program continuing? It should have continued normally (though it is not good practice to have big ERROR messages scrolling across the screen:) On 03/01/2017 02:58 PM, Gustav Mårtensson wrote: > > Hi, > > Yes, the buildstamp says > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c and running > Ubuntu 16.04.1 LTS: > > $ lsb_release -a > LSB Version: > core-9.20160110ubuntu0.2-amd64:core-9.20160110ubuntu0.2-noarch:security-9.20160110ubuntu0.2-amd64:security-9.20160110ubuntu0.2-noarch > Distributor ID: Ubuntu > Description: Ubuntu 16.04.1 LTS > Release: 16.04 > Codename: xenial > > Running it on another computer with Ubuntu 14.04 and FS 6.0 produces > the same error. > > *Gustav Mårtensson* | PhD student > Division of Clinical Geriatrics > Department of Neurobiology, Care Sciences and Society > Karolinska Institutet > > On 2017-03-01 19:00, Douglas N Greve wrote: >> And this is in version 6? What platform are you using? >> >> >> On 03/01/2017 12:07 PM, Gustav Mårtensson wrote: >>> Hi, >>> >>> Yes, running mri_convert >>> ADNI_032_S_0187_MR____________MPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm >>> dummy.mgh still produces the error >>> >>> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 >>> DICOM File: >>> /home/gustav/Desktop/0e242a36-5390-4358-9f92-eb9f62c48124/ADNI_032_S_0187_MR____________MPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm >>> break DICOMRead.c:5228 >>> >>> regardless of if the dicom file is in its own directory or not. >>> >>> Best, >>> Gustav >>> >>> On 2017-03-01 17:47, Douglas N Greve wrote: >>>> Yes. I cannot replicate the error on my end. If you copy that dicom file >>>> to its own directory and try to convert it, do you get the same error? >>>> >>>> doug >>>> >>>> ps. Please include previous correspondence. >>>> >>>> >>>> On 03/01/2017 02:54 AM, Gustav Mårtensson wrote: >>>>> Hi Douglas, >>>>> >>>>> Thank you for your reply! I've attached one of the dicoms that fails. >>>>> >>>>> setenv FS_LOAD_DWI 0 removes the error. Would you recommend doing this >>>>> over replacing the mri_convert binary in FS 6.0 with the one from FS >>>>> 5.3.0. >>>>> >>>>> Best regards, >>>>> Gustav >>>>> It looks like it found something that it thinks is a DWI parameter >>>>> butisn't, and it is causing it to fail. Can you send me one of the >>>>> dicoms?In the mean time, if yousetenv FS_LOAD_DWI 0 then the error should go away >>>>> >>>>> On 2/28/17 8:33 AM, Gustav Mårtensson wrote: >>>>> >>>>> Hi, >>>>> >>>>> I have a problem when executing the following command on >>>>> imagesscanned on 1.5T Philips (Intera) in FS 6.0:recon-all >>>>> -i0e242a36-5390-4358-9f92-eb9f62c48124/ADNI_032_S_0187_MR____________MPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm-subjid >>>>> 4450a7a0-27e9-42bc-99ab-1c15519ad9a4 -all -mprage >>>>> -qcache-hippocampal-subfields-T1 -brainstem-structures -cw256 >>>>> >>>>> which during mri_convert produces the error: >>>>> >>>>> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 >>>>> >>>>> DICOMs from other scanners works fine as far as we know. >>>>> Whenprocessing them through 5.3.0 we didn't get any errors like >>>>> this,regardless of scanner If we just copy the mri_convert >>>>> binary file fromFS 5.3.0 to FS 6.0 the errors disappears. Would >>>>> this be the recommendapproach to solve our issues?We are running >>>>> on Ubuntu 16.04 LTS with FS >>>>> versionfreesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. >>>>> I'veincluded recon-all.log case it is of interest. >>>>> >>>>> Thank you for your help! >>>>> >>>>> -- >>>>> *Gustav Mårtensson* | PhD student >>>>> Division of Clinical Geriatrics >>>>> Department of Neurobiology, Care Sciences and Society >>>>> Karolinska Institutet >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> _______________________________________________ Freesurfer mailing >>>>> listFreesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> <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 >>>>> <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. >>>>> -- >>>>> *Gustav Mårtensson* | PhD student >>>>> Division of Clinical Geriatrics >>>>> Department of Neurobiology, Care Sciences and Society >>>>> Karolinska Institutet >>>>> >>>>> >>>>> >>>>> ___________________________________ >>>>> Karolinska Institutet – a medical university > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(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/

1 0

"Upgrade" outputs from 5.3 to 6.0
by Chris Adamson 02 Mar '17

02 Mar '17

Is it possible to run Freesurfer 6.0 recon-all -all on a subject previously processed with 5.3 and have 6 utilise the wm, ctrl pt and pial edits (brainmask.finalsurfs.manedit.mgz) made in the 5.3 output? Would it be ok to run -autorecon2-wm -autorecon3 after renaming aseg.mgz to aseg.presurf.mgz? Thanks in advance? Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children’s Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au<http://www.mcri.edu.au/> E chris.adamson(a)mcri.edu.au T 03 9936 6780 ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

2 1

how convert GIFTI format file
by Flavia Arduini 02 Mar '17

02 Mar '17

I have GIFTI (.gii) format file resulting from segmentation with cat 12 ( toolbox of spm). How can I convert? with mris_convert function I can not convert them. can someone help me? Thanks Flavia Arduini

2 1

Re: [Freesurfer] Creating custom aparc.a2009s+aseg.mgz: Shuffled names of parcellations after mris_label2annot
by Antonin Skoch 02 Mar '17

02 Mar '17

Dear Doug, thank you, adding --no-unknown indeed fixed the global shuffling of the label names. However, last line of .ctab seems not to be read this time and produced .annot does not contain perirhinal label. My modified .ctab file looks like this: 0 Unknown 0 0 0 0 1 G&S_frontomargin 23 220 60 0 2 G&S_occipital_inf 23 60 180 0 3 G&S_paracentral 63 100 60 0 4 G&S_subcentral 63 20 220 0 5 G&S_transv_frontopol 13 0 250 0 6 G&S_cingul-Ant 26 60 0 0 7 G&S_cingul-Mid-Ant 26 60 75 0 8 G&S_cingul-Mid-Post 26 60 150 0 9 G_cingul-Post-dorsal 25 60 250 0 10 G_cingul-Post-ventral 60 25 25 0 11 G_cuneus 180 20 20 0 12 G_front_inf-Opercular 220 20 100 0 13 G_front_inf-Orbital 140 60 60 0 14 G_front_inf-Triangul 180 220 140 0 15 G_front_middle 140 100 180 0 16 G_front_sup 180 20 140 0 17 G_Ins_lg&S_cent_ins 23 10 10 0 18 G_insular_short 225 140 140 0 19 G_occipital_middle 180 60 180 0 20 G_occipital_sup 20 220 60 0 21 G_oc-temp_lat-fusifor 60 20 140 0 22 G_oc-temp_med-Lingual 220 180 140 0 23 G_oc-temp_med-Parahip 65 100 20 0 24 G_orbital 220 60 20 0 25 G_pariet_inf-Angular 20 60 220 0 26 G_pariet_inf-Supramar 100 100 60 0 27 G_parietal_sup 220 180 220 0 28 G_postcentral 20 180 140 0 29 G_precentral 60 140 180 0 30 G_precuneus 25 20 140 0 31 G_rectus 20 60 100 0 32 G_subcallosal 60 220 20 0 33 G_temp_sup-G_T_transv 60 60 220 0 34 G_temp_sup-Lateral 220 60 220 0 35 G_temp_sup-Plan_polar 65 220 60 0 36 G_temp_sup-Plan_tempo 25 140 20 0 37 G_temporal_inf 220 220 100 0 38 G_temporal_middle 180 60 60 0 39 Lat_Fis-ant-Horizont 61 20 220 0 40 Lat_Fis-ant-Vertical 61 20 60 0 41 Lat_Fis-post 61 60 100 0 42 Medial_wall 25 25 25 0 43 Pole_occipital 140 20 60 0 44 Pole_temporal 220 180 20 0 45 S_calcarine 63 180 180 0 46 S_central 221 20 10 0 47 S_cingul-Marginalis 221 20 100 0 48 S_circular_insula_ant 221 60 140 0 49 S_circular_insula_inf 221 20 220 0 50 S_circular_insula_sup 61 220 220 0 51 S_collat_transv_ant 100 200 200 0 52 S_collat_transv_post 10 200 200 0 53 S_front_inf 221 220 20 0 54 S_front_middle 141 20 100 0 55 S_front_sup 61 220 100 0 56 S_interm_prim-Jensen 141 60 20 0 57 S_intrapariet&P_trans 143 20 220 0 58 S_oc_middle&Lunatus 101 60 220 0 59 S_oc_sup&transversal 21 20 140 0 60 S_occipital_ant 61 20 180 0 61 S_oc-temp_lat 221 140 20 0 62 S_oc-temp_med&Lingual 141 100 220 0 63 S_orbital_lateral 221 100 20 0 64 S_orbital_med-olfact 181 200 20 0 65 S_orbital-H_Shaped 101 20 20 0 66 S_parieto_occipital 101 100 180 0 67 S_pericallosal 181 220 20 0 68 S_postcentral 21 140 200 0 69 S_precentral-inf-part 21 20 240 0 70 S_precentral-sup-part 21 20 200 0 71 S_suborbital 21 20 60 0 72 S_subparietal 101 60 60 0 73 S_temporal_inf 21 180 180 0 74 S_temporal_sup 223 220 60 0 75 S_temporal_transverse 221 60 60 0 76 entorhinal_exvivo.thresh 222 62 67 0 77 perirhninal_exvivo.thresh 223 65 60 0 with newline in the end. However, I was able to successfully generate annotation with 2 labels ( previous swap of names in .annot produced using --l options was my fault since I did not read the help to the detail to learn that the order of label files of --l arguments has to match the order of names in .ctab). So I could possibly achieve my goal by run mri_aparc2aseg on this simple 2-label annot and somehow merge the result with the default aparc.a2009s to bring the rhinal labels into that. Do you see any pitfall with that? In any case, however, before running aparc2aseg I have to cope with another problem with rhinal labels - the rhinal.thresh labels are overlapping and I would need to correctly assign vertices in the label intersection (see my previous post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51919.html ). Regards, Antonin Try adding --no-unknown to the label2annot command line On 02/28/2017 04:45 PM, Antonin Skoch wrote: > Dear experts, > > I would like to create modified aparc.a2009s+aseg file with relevant > parts of parahippocampal cortical ribbon voxel labels replaced by > labels derived from surface labels of entorhinal and parahippocampal > cortex (created also by default in recon-all). This modified > aparc.a2009s+aseg file I want to use for streamline assignment in > structural connectome generation in MrTrix3. > > I think that mri_label2vol is not optimal way to do it since it would > leave some voxels in the ribbon unassigned. > > I think that the better, but much complicated, way to do this is to > modify aparc.a2009s.annot with the information from these labels and > then run again mris_aparc2aseg. > > I tried to do this by using: > > mri_annotation2label > > and > > mris_label2annot --hemi lh --subject my_subject --ldir my_labels --a > my_aparc.a2009s --ctab my_aparc.annot.a2009s.ctab --debug > > I took the aparc.annot.a2009s.ctab from the my_subject/label > directory and added to the end 2 row with entorrhinal and perirhinal > parcellations with unique RGB values to assure the relevant parts of > parahippocampal gyrus label are replaced by these new labels I want to > supply. > > But the resulting new .annot file is not correct - the labels are in > correct position on cortical surfaces, but the label names of all > labels are shuffled. > > I even tried the sequence of mri_annotation2label, mris_label2annot > without adding new labels, just converting annotation to labels and > back, and the annotation naming is also corrupted. > > I also tried to create new annotation just from 2 new labels, > preparing .ctab file and running mris_label2annot by explicitly > specifying my 2 labels like > > mris_label2annot --hemi lh --subject my_subject --l > lh_labels/lh.perirhinal_exvivo.thresh.label --l > lh_labels/lh.entorhinal_exvivo.thresh.label --a rhinal_aparc.a2009s > --debug --ctab rhinal_aparc.annot.a2009s.ctab > > In this case the label names in annotation are swapped (entorhinal is > perirhinal and vice versa), swapped are also file names of labels > which I tried to back convert by using mri_annotation2label. > > I am using quite recent build of dev version of Freesurfer from > 28/2/2017. > > Could you suggest where could be the problem? > > Or could you advice different, possibly more simple way, how to > achieve my goal? > > Thank you in advance. > > Regards, > > Antonin Skoch

2 1

Re: [Freesurfer] wm.mgz manual editing
by Rockers, Elijah D. 02 Mar '17

02 Mar '17

Bruce, Main problem area that I can see is at coordinates [104,42,124]. My first attempt, I don't think I had the recon editing box checked when I was editing the white matter, but I used a brush value of 255. My second attempt I painted over the same voxels but with the recon editing box checked. Both times, after saving wm.mgz I ran the following command: "recon-all -autorecon2-wm -autorecon3 -subjid my_subject -sd `pwd`" Only thing different from the guide is I specify a different subject directory. Below are download links for the important files, let me know if you would like to look at anything else. If you look at wm.mgz along with the rh.white, you can see the surface doesn't appear to acknowledge my edit. 001.mgz: https://1drv.ms/u/s!AoOsIIayCH7qlxLBNvCT4JCvM1Kc recon-all.logs.tar.gz: https://1drv.ms/u/s!AoOsIIayCH7qlxRGOWpUCttk5Zji brainmask+surf+wm.tar.gz https://1drv.ms/u/s!AoOsIIayCH7qlxbDSS54gfHkq2M3 Thanks tremendously for your time, Eli > ------------------------------ > > Message: 4 > Date: Wed, 1 Mar 2017 16:39:33 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] wm.mgz manual editing > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <https://urldefense.proofpoint.com/v2/url?u=http-3A__alpine.LRH.2.20.1703011… > > Content-Type: text/plain; charset="utf-8" > > Hi Eli > > hmm, maybe you should just upload the subject and email us the voxel > coords you are talking about? > > Also, in general it is hard for us to help you unless you include more > information. What exact command did you run? What was the screen output? > What was in the recon-all.log? > > cheers > Bruce > > > On Wed, 1 > Mar 2017, Rockers, Elijah D. wrote: > > > Couple of questions: > > > > 1) > > > > I edited wm.mgz following the instructions in the wiki guide, but it did > > not change anything after reconstruction. I am still using 5.3 right > > now, so maybe the guide is wrong for me. What is the brush value > > supposed to be? I used 255 but it did not extend the white matter > > surface to include my edits. I checked to make sure they saved > > correctly, they did, but the surface didn't change. Any ideas? > > > > 2) > > > > The reason I am editing wm.mgz is to try to include some cortex that was > > left out of the pial surface. I don't suppose there's any way to fix > > this without editing wm.mgz? Because the white matter surface actually > > looks fine the way it is. > > > > Thanks, > > Eli > > > > Houston Methodist. Leading Medicine. > > Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also 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.

1 0

FreeSurfer v6.0 in an AWS cloud configuration (hipposubfield/brainstem failures)
by randrews＠admdx.com 02 Mar '17

02 Mar '17

1 0

Invalid FreeSurfer license key "sometimes"
by anna calvo 02 Mar '17

02 Mar '17

Hello FreeSurfer Developers, We are attempting to install Freesurfer 5.3 on a server. We have an odd problem. When we run any FS command from this server we get a license error: Invalid FreeSurfer license key found in license file /opt/Ngs_analysis/programs/freesurfer/5.3/freesurfer/.license But when the same freesurfer called from another server we can run freesurfer without problems. So we think that maybe is an error from the eviroment. The server where FS is installed is suse 2011 and the server where run FS instructions and works is centos 2017. I don't know if it helps. Also we have a problem apptempting to install Freesurfer 6.0 on that sever we allways get a license error wherever we call it. I've searche the list and no similar errors have been reported. Does anyone have any thought on ho to trouble-shoot this one? Also, I've attached the recon-all.log and enviroment infromation. 1)FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0, we don't find any other version. We have freesurfer runing in other machine with suse also freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 but in version file is write freesurfer-x86_64-redhat-linux-gnu-stable5-20130513 either in the version file of our server is write freesurfer-x86_64-unknown-linux-gnu-stable5-20130513. In the website I just see for dowloading centos version and in the email list says that is not tested but people says that no have problems. 2)Platform: SUSE LINUX Release: 11 Codename: n/a 3)uname -a: Linux BioNGS1 3.0.101-0.7.17-default #1 SMP Tue Feb 4 13:24:49 UTC 2014 (90aac76) x86_64 x86_64 x86_64 GNU/Linux 4)recon-all.log, enviroment: see attached thanks in advance, anna

2 1

threshold method used to obtain *exvivo.thresh.labels
by Antonin Skoch 01 Mar '17

01 Mar '17

Dear experts, Could you please provide me the information how exactly the *_exvivo.thresh.labels have been thresholded? According to this post, http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32542.html .thresh labels are thresholded to pick the most likely vertices that give a label that is the right surface area.But how they are thresholded in the boundary of the region where the unthresholded labels do not overlap? There must be additional threshold applied: For example for BA45 there is no further BA label towards frontal pole, but the BA45_exvivo.thresh.label is also restricted in this region wrt BA45_exvivo.label. I have further question concerning used thresholding method of perirhinal_exvivo.thresh and entorhinal_exvivo.thresh labels. It seems that this method is not applied here since looking at them at the fsaverage surface, they are overlapping. And also *rhinal_exvivo.labels are much more extending to the adjacent regions than *rhinal_exvivo.thresh.labels. What method is applied here? My main objective to obtain annotation with the vertices properly assigned to perirhinal_exvivo and entorhinal_exvivo to supply this annotation to mri_aparc2aseg to assign ribbon voxels to that parcellation. I think I could use mris_label2annot --maxstatswinner with unthresholded entorhinal and perirhinal labels to assign vertices to most probable label, but I would need to further threshold the labels by correct value to obtain results similar in extent to thresh.labels. For perirhinal, it seems that the additional threshold is 0.4 (what is rationale for this value?), for entorhinal it seems also around 0.4 but could not find any particular threshold to obtain the exact shape of label corresponding to entorhinal_exvivo.thresh. Thank you in advance for clarification. Regards, Antonin Skoch

1 0

Re: [Freesurfer] multiple expert options files/ wm and control points
by Antonin Skoch 01 Mar '17

01 Mar '17

Dear Paul, 1) You find pretty thoroughful info on expert options file here: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences 2) recon-all -autorecon2-cp -autorecon3 is ok (btw -autorecon2-cp and -autorecon2-wm runs the same commands, at least in version 6.0). 3) There is in the souce code following comment on -T option in mri_fill: min # of neighbors which must be on to retain a point Default value is 1. Regards, Antonin Hello Freesurfer, I have couple questions. 1) If I have 2 commands (e.g., mri_normalize -a 30 and mris_inflate -n 30) and I want recon-all to execute both commands. Should I create 2 different expert opts files or 1 expert opts file with both commands in it? Also, how do I include the expert flag with recon? 2) If I have added control points and wm edits to a subject, it is accurate to start from control points? i.e., recon-all -autorecon2-cp -autorecon3 3) Lastly, I am playing around with mri_fill command and I did like to know what -T flag does? Thank you Best, Paul

4 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