Freesurfer

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30132 discussions

Re: [Freesurfer] Fwd: wm edits not incorporated
by Antonin Skoch 13 Apr '17

13 Apr '17

Dear Octavian, the current philosophy with wm.mgz edits is not to directly affect voxel values in original T1 image. The wm.mgz serves as starting point for the white surface estimation. The ?h.white surface is estimated according gradient in voxel values in brain.finalsurfs.mgz (which is, basically, preprocessed T1 image) using basically preprocessed surfaces obtained from wm.mgz (?h.orig) as a starting position where to search for intensity gradient. The editing of wm.mgz helps to find out the GM/WM itensity gradient and properly place ?h.white there. Therefore, where there is insufficient GM/WM contrast, the wm.mgz cannot help out. I think that there is no change in the behavior between v5.3 and v6.0 in this aspect. I have seen many cases where wm.mgz edit does not help to improve ?h.white surfaces in the data processed by v5.3. There is an -overlay option in mris_make_surfaces which explicitly modifies voxel values in input image for mris_make_surfaces (brain.finalsurfs.mgz as default in recon-all). However, this option only works for cases when wm.mgz is extended, not deleted: In voxels which have value 255 in wm.mgz, it replaces current voxel value in input image by desired value of white matter. This option is currently not used in recon-all. I would opt for implementation of similar option for deletion of voxels in wm.mgz: Where wm.mgz voxel values equal 1, to replace input image voxel values by desired values of GRAY matter. This should force ?h.white to directly follow edits of wm.mgz As for editing of 001.mgz, beware the pitfall with editing images with mutually different geometry in FreeView I posted today: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52729.html Antonin Skoch Dear All, Regarding wm.mgz edits not incorporated into wm surface, which seems to have been reported on by several of us with FS 6.00. I followed Antonin's idea of editing 001.mgz by switching wm-intensity voxels clearly not wm (mostly in the subtemporal regions, at times close to bright dural portions in the crown) to gm intensities and ran recon-all -all, and this time all was OK. So it seems that the problem is that on re-initializing during -autorecon2-wm rerun, the routine does not edit out high intensity voxels even if manually excluded in wm.mgz. This seems to be different to some extent with how FS 5.3 was reacting, although I did not look at this systematically. There may be a reason that manual editing is just part of the story during rerun and does not automatically override the recon stream, but I do not know it. Octavian ---------- Forwarded message ---------- From: Octavian Lie <octavian....(a)gmail.com> Date: Sun, Apr 2, 2017 at 7:59 PM Subject: wm edits not incorporated To: octavian lie <octavian....(a)gmail.com> Dear Bruce, I just transferred subject r02.tar.gz. Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated on reruns using any of the recon-all -autorecon-wm -aitorecon3 recon-all -autorecon2 -autorecon3 recon-all -make all FOr example, the complete command line for a rerun is recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02 -parallel > output.txt & Here are some of the edited voxels which are not excluded from the wm on rerun: -40.14, -2.67, 116.29 coronal slice 132 12.73, -23.67, 126.16 coronal slice 171 14.05, 12.33, 11.61 coronal slice 147

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Re: [Freesurfer] Freeview - corrupted pixel values after saving volume (via save as) when images with mutually different geometry are simultaneously loaded
by Antonin Skoch 13 Apr '17

13 Apr '17

Dear Ruopeng, thank you for the feedback. Yes, the behavior is exacly like you described. I suspected that this has something to do with resampling but I was not sure. The stripes were result of nearest-neighbor interpolation. Antonin Hi Antonin, When you load two images like that, the second image will be resampled, using nearest neighbor method by default. And when you save, it will be resampled back to its original space. So there will be shifted voxels depending how oblique it is to the first image. So I think what you observe makes sense. That is also why you should always edit volumes in their local space. I didn't find any screenshots in your last email but my guess is the oblique strip is due to nearest neighbor resampling. You can choose "-trilinear" or "-cubic" in the command line when you load the images. Best, Ruopeng On 04/13/2017 12:28 PM, Antonin Skoch wrote: Dear experts, I encountered following issue with freeview: When two images with mutually different geometry are simultaneously loaded and one of them is saved (via save as), its pixel values get somewhat corrupted. There are strips in image with modified pixel values. It seems to affect only the latter image in the pair. Example (001.mgz and brainmask.mgz have different geometry): freeview brainmask.mgz orig/001.mgz Then I saved 001.mgz as 001_2.mgz (using "save as") and loaded 001_2.mgz to freeview. The attached screenshots show original 001.mgz and 001_2.mgz with corrupted pixels. Note new oblique strips. This is not only display issue. The mri_diff 001.mgz 001_2.mgz outputs: diffcount 287447 Volumes differ in pixel data maxdiff 966.00000000 at 171 255 30 0 I am using recent development version of freesurfer from 04/2017. Regards, Antonin Skoch

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Surface down sample by taking cortical vertices only
by Dorothy Sincasto 13 Apr '17

13 Apr '17

Hi I want to do an MEG analysis and first I want to downsample the surface to around 100 vertices per hemisphere. I tried the command mris_downsample, but when i plot the surface I see that the vertices go deep into the white matter. Is there an option to extract for example 100 equidistant vertices from a fsaverage? Maybe knowing how the vertices are organized when saved would help, so for example, when I load a surface in matlab the vertices are shown as a vector, is there a way to know the spatial order? Thanks Dorothy

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Freeview - corrupted pixel values after saving volume (via save as) when images with mutually different geometry are simultaneously loaded
by Antonin Skoch 13 Apr '17

13 Apr '17

Dear experts, I encountered following issue with freeview: When two images with mutually different geometry are simultaneously loaded and one of them is saved (via save as), its pixel values get somewhat corrupted. There are strips in image with modified pixel values. It seems to affect only the latter image in the pair. Example (001.mgz and brainmask.mgz have different geometry): freeview brainmask.mgz orig/001.mgz Then I saved 001.mgz as 001_2.mgz (using "save as") and loaded 001_2.mgz to freeview. The attached screenshots show original 001.mgz and 001_2.mgz with corrupted pixels. Note new oblique strips. This is not only display issue. The mri_diff 001.mgz 001_2.mgz outputs: diffcount 287447 Volumes differ in pixel data maxdiff 966.00000000 at 171 255 30 0 I am using recent development version of freesurfer from 04/2017. Regards, Antonin Skoch

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Re: [Freesurfer] manual edits
by Antonin Skoch 13 Apr '17

13 Apr '17

Dear John, David, To great summarization of David, I would add following: My personal preference is to run whole -autorecon2 -autorecon3 after editing of the brainmask.mgz. Early stages of -autorecon2 (normalization, registration, volumetric labeling) use brainmask.mgz, therefore I believe that their results can be improved when improved brainmask.mgz is provided (especially when the edits of the brainmask.mgz are of large extent). When the pial surface extends to the cerebellum, different edits are needed as specified here: http://freesurfer.net/fswiki/FsTutorial/PialEdits_freeview Antonin Skoch Hi David, Thank you for the feedback! I followed your advice's and everything has been resolved. Highly appreciated!Cheers, John Sent with [ProtonMail](https://protonmail.com) Secure Email. -------- Original Message -------- Subject: Re: [Freesurfer] manual edits Local Time: April 12, 2017 11:04 AM UTC Time: April 12, 2017 3:04 PM From: seman...(a)nyspi.columbia.edu To: John Anderson <john.ande...(a)protonmail.com>, freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Hi John, Yes understanding how freesurfer deals with edits can be a bit confusing. I have a lot of experience doing edits to the wm.mgz and brainmask.mgz for cross sectional data in Freesurfer 5.3 so perhaps I can help. Recon-all is basically a script which runs a series of about 25 or so processing steps in a defined sequence. The software generally will be able to recognize when an edit has been done at a particular intervention point and will take those edits into account when running that step unless you specifically instruct it not to. The most common types of edits are edits to the wm.mgz to fix white matter defects and tissue incorrectly identified as white matter, and edits to the brainmask.mgz to fix cases where the skull strip is insufficient to prevent dura and other non-cortical tissue from making it into the gray matter/pial surfaces. White matter edits need to be done directly on the wm.mgz and gray matter/skull strip edits need to be done on the brainmask.mgz. Editing those two files and saving them directly in freeview is sufficient to register those edits for recon-all. If you have edited only the brainmask.mgz, it is sufficient to run –autorecon-pial since the white matter surfaces will not need to be regenerated. If you have edited the wm.mgz, you must run –autorecon2-wm (or –autorecon2-cp if you used control points as well as white matter edits). If you have edited both the brainmask.mgz and the wm.mgz, then you only need to run –autorecon2-wm since the pial surfaces will be regenerated taking into account the brainmask.mgz edits as part of that workflow. Keep in mind that you still need to run –autorecon3 to complete the reprocessing of these data (-autorecon-pial includes the steps from –autorecon3) but that can be done when you are happy with your final surfaces if you want to save processing time on iterative edits. Here is the wiki page referring to edits: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData I hope this is helpful. Best, David P. Semanek, HCISPP Research Technician, Posner Lab Division of Child and Adolescent Psychiatry Columbia University Medical Center New York State Psychiatric Institute 1051 Riverside Drive, Pardes Bldg. Rm. 2424 New York, NY 10032 PH: (646) 774-5885 IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From: John Anderson <john.ande...(a)protonmail.com> Reply-To: John Anderson <john.ande...(a)protonmail.com> Date: Wednesday, April 12, 2017 at 6:45 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] manual edits Dear Freesurfer experts, I am not an expert in manual edits, so I highly appreciate any feedback regarding the issues in my questions below. I ran the following command line “recon-all -s subjid -all” on T1 image for one of the subjects. when reviewing the output images (i.e. wm.mgz, brainmask.mgz) I found issues as attached. Attached is an output of the command: "Freeveiw orig.mgz wmparc.mgz wm.mgz" 1. When I reviewed “wm.mgz” I see interactions between the white matter (wm), and the cortex (yellow arrows). To fix this, I edited “wm.mgz” by removing the wm voxels from the cortex, and the data was saved in the file “wm.seg.mgz” 2. I found many holes in many slices similar to the (black arrow). I filled all these holes. The data saved in “wm.seg.mgz” 3. I fixed some issues related to dura and bad skullstipping Then I ran the command: “recon-all -autorecon2-wm -autorecon3 -subjid <subject>” which output the file “brain.finalsurfs.mgz” and the command “recon-all -autorecon-pial -subjid <subject>” Now, I want to understand where Freesurfer implement the new edits? Which files will be used as the main files that include the new edits. Logically, the edits must be implemented in "wm.mgz" and "brainmask.mgz". What confuses me is when I open orig.mgz wm.mgz and brainmask.mgz in freesview. I see the original non-edited files. I am not sure what I am doing wrong so I highly appreciate any help. John

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trac-all -stat
by Versace, Amelia 13 Apr '17

13 Apr '17

Hi Anastasia, I am having some issues with the -stat option. Below is the error. I am not sure of what's causing the issue. Any idea? Thanks a lot!! Amelia ----------------- trac-all -c scripts/dmrirc.stats -stat INFO: SUBJECTS_DIR is /data/dprojects/BIOS/freesurfer INFO: Diffusion root is /data/dprojects/BIOS/tracula Actual FREESURFER_HOME /data/software/freesurfer6 ERROR: no pathway reconstructions found ---------------------

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Bits of dura being captured as GM ..
by Shane S 13 Apr '17

13 Apr '17

Hi Freesurfer Users, I am checking my data and there are many scans with a bit of dura being captured as GM. I have attached some screenshots below. This happens in more than 50% of my subjects. I am removing them manually them using Freeview, then running the autorecon-pial. But this will take a lot of time on 200+ subjects.. Does anyone have any tips to deal with these little inclusions? Thanks =) Best Wishes, Shane

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mri_watershed script not working
by Mario Rossi 13 Apr '17

13 Apr '17

Hello FreeSurfer Developers and experts, I am trying to run our FSPGR sequences using the -mri_watershed script, but I am not able to set and vary the -t threshold. The aim of my work is to calculate the BPF in order to quantify parenchymal atrophy in patients with Multiple Sclerosis. Instead of using the whole "-recon-all" command, I have tried to reduce the amount of datas (and the very long time needed to calculate them) performing this script: "-mri_watershed -atlas" The result of the extraction of the brain is good and fast, but I still could need to adjust the cut limits. I have tried to modify it into this new script: "-mri_watershed -atlas -t X" (where "X" stands for a variable between 0 and 50) but in this case, no matter what "X" I choose the results are all identical. Is it possible to set a -t threshold using -atlas? If not, can you suggest us how to change our approach? Is it possibile to use freesurfer with FLAIR sequences with the same aim (extract the BPF to evaluate brain atrophy)? Best regards, Mario Rossi 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Linux Mint 1 Debian MATE 64-bit

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error from annot file : 7607 vertices did not have an annotation!
by Das S. 13 Apr '17

13 Apr '17

Dear FreeSurfer Developer, I have created my own atlas file and from the atlas file created the annot file. When I am trying to load my annot file on the sphere surface and view in tksurfer, I am getting below error: 7607 vertices did not have an annotation! I have the below steps in sequence: 1. I am creating my label files from matlab and keeping them in a folder. 2. From the labelled files I am creating the annot file using the below command: mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/MyColorLUTnew.txt --a eqnew40aparc --ldir 100307/label/eq_parcellation_label/ 3. When I am loading this lh.eqnew40aparc.annot file on sphere surface in tksurfer , it showing me all labels perfectly. tksurfer 100307 lh sphere 4. Then I am creating the .gcs file from the annot file using below command. The gcs files is being created without any error . mris_ca_train -t 100307/label/eq_parcellation_label/MyColorLUT.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.left40aparc.annot 100307 100307/label/lh.reg40aparc.gcs 5. Then I am creating the .annot file using the my created atlas file using the below command: mris_ca_label -l 100307/label/lh.cortex.label -aseg 100307/mri/aseg.presurf.mgz 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.eqnew40aparc.gcs 100307/label/lh.aparc.annot using 100307/mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from 100307/label/lh.eqnew40aparc.gcs... reading color table from GCSA file.... average std = 0.2 using min determinant for regularization = 0.001 0 singular and 194 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 572 labels changed using aseg relabeling using gibbs priors... 000: 284 changed, 133181 examined... 001: 8 changed, 1741 examined... 002: 0 changed, 37 examined... 2 labels changed using aseg 000: 67 total segments, 24 labels (284 vertices) changed 001: 44 total segments, 1 labels (2 vertices) changed 002: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... 0 vertices marked for relabeling... 0 labels changed in reclassification. writing output to 100307/label/lh.aparc.annot... classification took 0 minutes and 6 seconds. koushik@koushik-DQ77MK:~/Parcellation$ 6. Now when I am trying to see this file in tksurfer loading as annot file on sphere surface I can see a big patch of gray color and showing me the message : 7607 vertices did not have an annotation! [X] I am attaching the .annot file , .gcs file and colortable .Plase help me to understand where the thing is going wrong,Any help will be much appreciated. Thanks & regards Sarbani

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mris_ca_label giving error CTABfindAnnotation: ct was NULL
by Das S. 13 Apr '17

13 Apr '17

Hi, I have created a color table, an annot file and a .gcs file( attached with the mail). But when I am trying to execute mris_ca_label with my own .gcs file I am getting the error : mris_ca_label -l 100307/label/lh.cortex.label -aseg 100307/mri/aseg.presurf.mgz 100307 lh lh.sphere.reg 100307/label/lh.eq40aparc.gcs lh.aparc.annot using 100307/mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from 100307/label/lh.eq40aparc.gcs... average std = 0.2 using min determinant for regularization = 0.001 0 singular and 185 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory ..... Before this I have used the below commands, to sucessfully create the .annot and .gcs file: 1. To create .annot file from label files and CTAB file-- mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/MyColorLUT.txt --a eq40aparc --ldir 100307/label/eq_parcellation_label 2. To crate .gcs file from annot file. mris_ca_train rh 100307/surf/rh.sphere 100307/label/rh.eq40aparc.annot 100307 100307/label/rh.eq40aparc.gcs I am not be able to understand where is the problem. Any help will be appreciated. Thanks Sarbani

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