[Freesurfer] Visualizing specific cortical parcels in Desikan Killiany atlas
External Email - Use Caution Dear experts, I have a basic visualization question. I would like to create a surface brain figure with specific cortical parcels colored. Similar to https://secure-web.cisco.com/1DryTPj2WrD-LULa8TF6HVh2xwKTLAaWDFvIpAUrs4z6O2VOFttAjezDQX2aR4Z5m6bFRIWk8l6q3Kc0B4K1EjsGa3Ps7AUkb5SPODPx-r-FwnmCtHYHHKbdbpiaWUNhY_vlBvQaG-4Cl9kGxomgOLjtwUjpfxAwjLULtd8raS9pKKnnCsUkx0wW3RSuyX62NEemue5GJ8QZ5J46l4PfzCFjifys8EQeNVKxstOck3xiE-BXhju-kVWs7GQxLXjjk6zMrtaHPswi0sl3CPcqM2A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview%3Faction%3DAttachFile%26do%3Dget%26target%3Dgood_output_aparc_crop.png but not with ALL parcels in the atlas selected. I know that I can go into a subject folder and load this freeview -f surf/lh.pial:annot=aparc.annot in order to see the entire Desikan Killiany atlas. However, I would like to select 4-5 rois. What's the best way to do this? It won't be related to any results and doesn't need to be from a particular subject's brain (can also be fsaverage). It's purely to highlight some cortical parcels for visualisation purposes. Thanks, Ellen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_fix_topology taking ages
External Email - Use Caution thanks Bruce and Douglas, I was able to see the holes by looking at the surface of ?h.smoothwm.nofix and I found the Freesurfer tutorial on how to correct topological defects. However, as the automatic topology fixer runs during recon-all, how do we know that it failed? I see "CORRECTING DEFECT" for multiple defects in the recon-all.log, so I'm assuming it's fixing those holes. How can I determine whether it's worth it to go in and manually fix them? Is there an indication somewhere? Thank you! On 6/2/2021 4:40 PM, Fischl, Bruce wrote: Hi Diana It’s not the number of defects that matters – it is the large ones. The time it takes to correct them is square in the (convex hull of the) number of vertices in the defect. We have a tutorial on our website about how to find them and fix them. I find it easiest to load the ?h.orig.nofix over the wm.mgz and norm.mgz then load the ?h.defect_labels to onto the ?h.orig.nofix to color the vertices that are in a defect Cheers Bruce *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *DIANA ORTEGA CRUZ *Sent:* Wednesday, June 2, 2021 3:12 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] mris_fix_topology taking ages *External Email - Use Caution * Dear Douglas and Bruce, my name is Diana, I am encountering the same issue as Ellen with Fix-topology taking too long. Once we make sense of the origin of the issue (for example, I confirmed that my smoothwm.nofix has a lot of holes), do you know if is there any way to solve it? Could the data be modified in some way to get through this step? Thanks a lot for your great help!! Best wishes, Diana Ortega. El mié, 2 jun 2021 a las 3:13, Fischl, Bruce (<mailto:bfis...@mgh.harvard.edu>>) escribió: Or the ?h.inflated.nofix can be helpful as well *From:* freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of *Douglas N. Greve *Sent:* Tuesday, June 1, 2021 5:57 PM *To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] mris_fix_topology taking ages I mean mris_fix_topology. Try loading the ?h.smoothwm.nofix in surface viewing (not in the volume). You can often see defects better on this surface (they look likes holes or handles; you should at least see some) On 6/1/2021 4:55 PM, Ellen Ji wrote: *External Email - Use Caution * Hi Doug, when you say it did not finish, could you clarify what process "it" refers to? I loaded the files you suggested and nothing popped out to me aside from the fact that the wm.mgz didn't seem to cover all the white matter. Is it possible that topology error labels don't necessarily suggest that something went wrong and I can trust the results? Thanks. On 6/1/2021 2:51 AM, Douglas N. Greve wrote: The topology error labels might be be created if it did not finish. YOu can try just loading the brain.mgz, the wm.mgz, and the orig.nofix and see if you can find a big topo error On 5/31/2021 11:16 AM, Ellen Ji wrote: External Email - Use Caution Dear experts, mris_fix_topology has been running for several hours now and the log suggests many more defects than normal. I tried to follow Bruce's advice from the thread here https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_FJ9XkuZNLzTomdCZZwiiC6gS9oiXPNWh-M2KVbb9fP-1Qt7J-woH5hdLFg1otls4745ZoOKkz_-HOcFhenNfrq2-hdM_aX4I_g63u4rUe-NJLArGfWzCA77LLGm4lm0GK5kbCLf4Y6EqC9wHUUa-pdXC-7yMwNoi3Ips7HILVXXSdMEYlu_BPlUFIyI78yqCt3CSo6lAnlXS7QmRQY6JMl9WsV56bEMNqz44Bdlkw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg03182.html <https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_FJ9XkuZNLzTomdCZZwiiC6gS9oiXPNWh-M2KVbb9fP-1Qt7J-woH5hdLFg1otls4745ZoOKkz_-HOcFhenNfrq2-hdM_aX4I_g63u4rUe-NJLArGfWzCA77LLGm4lm0GK5kbCLf4Y6EqC9wHUUa-pdXC-7yMwNoi3Ips7HILVXXSdMEYlu_BPlUFIyI78yqCt3CSo6lAnlXS7QmRQY6JMl9WsV56bEMNqz44Bdlkw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg03182.html>, but wasn't able to load the _labels as I received the error below. Attached is part of the recon-all.log (starting from mris_fix_topology). Is there any other way to check/visualize what might have gone wrong? FYI, I'm running recon-all thru the HCP Pipeline. Thanks! tksurfer avoss_01 lh defect_labels subject is avoss_01 h
Re: [Freesurfer] mris_fix_topology taking ages
External Email - Use Caution Hi Doug, when you say it did not finish, could you clarify what process "it" refers to? I loaded the files you suggested and nothing popped out to me aside from the fact that the wm.mgz didn't seem to cover all the white matter. Is it possible that topology error labels don't necessarily suggest that something went wrong and I can trust the results? Thanks. On 6/1/2021 2:51 AM, Douglas N. Greve wrote: The topology error labels might be be created if it did not finish. YOu can try just loading the brain.mgz, the wm.mgz, and the orig.nofix and see if you can find a big topo error On 5/31/2021 11:16 AM, Ellen Ji wrote: External Email - Use Caution Dear experts, mris_fix_topology has been running for several hours now and the log suggests many more defects than normal. I tried to follow Bruce's advice from the thread here https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_FJ9XkuZNLzTomdCZZwiiC6gS9oiXPNWh-M2KVbb9fP-1Qt7J-woH5hdLFg1otls4745ZoOKkz_-HOcFhenNfrq2-hdM_aX4I_g63u4rUe-NJLArGfWzCA77LLGm4lm0GK5kbCLf4Y6EqC9wHUUa-pdXC-7yMwNoi3Ips7HILVXXSdMEYlu_BPlUFIyI78yqCt3CSo6lAnlXS7QmRQY6JMl9WsV56bEMNqz44Bdlkw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg03182.html, but wasn't able to load the _labels as I received the error below. Attached is part of the recon-all.log (starting from mris_fix_topology). Is there any other way to check/visualize what might have gone wrong? FYI, I'm running recon-all thru the HCP Pipeline. Thanks! tksurfer avoss_01 lh defect_labels subject is avoss_01 hemi is lh surface is defect_labels surfer: current subjects dir: /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf checking for nofix files in 'defect_labels' Reading image info (/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01) Reading /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz surfer: Reading header info from /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz nquads=4063237, nvertices=664 ERROR: MRISread: file '/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf/lh.defect_labels' has many more faces than vertices! Probably trying to use a scalar data file as a surface! No such file or directory ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1DI84rKL4SpDdiEv_m65JM6o4rI5AZVlICF1tso_GGIsz103u0f5eJKrymIzWHLYjyJhZ8OPhlD7r1ixMXxhz1Xz4rzrPA15mVVfHip72zyAWRosxKEOiQQzkQeM8llwv2GBAyT8OZgdtM-RAHQfqXClXeu50uqLv1CavAAGVNi2iTEJ8fTTWgOztEQmqU0DxU061XEn2hwSfyTYX_vDvgk2SmjaxOtaH1W2MdXO6Fy9JCvLeP0hjTVMM3VIkgAaqZryn5k7-YEGvP_diJKvhyw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1DI84rKL4SpDdiEv_m65JM6o4rI5AZVlICF1tso_GGIsz103u0f5eJKrymIzWHLYjyJhZ8OPhlD7r1ixMXxhz1Xz4rzrPA15mVVfHip72zyAWRosxKEOiQQzkQeM8llwv2GBAyT8OZgdtM-RAHQfqXClXeu50uqLv1CavAAGVNi2iTEJ8fTTWgOztEQmqU0DxU061XEn2hwSfyTYX_vDvgk2SmjaxOtaH1W2MdXO6Fy9JCvLeP0hjTVMM3VIkgAaqZryn5k7-YEGvP_diJKvhyw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1MbhuoBvdfG69ePlxn1Czlvrln1BpizbP_xFpnZqrml3kN8u9uqzSNvX_4Tn7UM9dBqnf0v4NW3LWuAb3umoPZDC2c1G79N6-vr2_BatVw_IVPr2RVWc3dbzh3CcsG6ZgyxemJnjf-4GTB-IEYYMlG6enFDA7Koxv9iqqL7spNhrioBA7IeASmhw25jO9VGUWv3MNoUTepPZ0UAYAk5t6jefwWvdpk4CcS-eO5P8dE8kXSKxzutdaWcnsABxozBzqHTH5ADWMK9N40IXCBiB1Mw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_fix_topology taking ages
External Email - Use Caution Dear experts, mris_fix_topology has been running for several hours now and the log suggests many more defects than normal. I tried to follow Bruce's advice from the thread here https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_FJ9XkuZNLzTomdCZZwiiC6gS9oiXPNWh-M2KVbb9fP-1Qt7J-woH5hdLFg1otls4745ZoOKkz_-HOcFhenNfrq2-hdM_aX4I_g63u4rUe-NJLArGfWzCA77LLGm4lm0GK5kbCLf4Y6EqC9wHUUa-pdXC-7yMwNoi3Ips7HILVXXSdMEYlu_BPlUFIyI78yqCt3CSo6lAnlXS7QmRQY6JMl9WsV56bEMNqz44Bdlkw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg03182.html, but wasn't able to load the _labels as I received the error below. Attached is part of the recon-all.log (starting from mris_fix_topology). Is there any other way to check/visualize what might have gone wrong? FYI, I'm running recon-all thru the HCP Pipeline. Thanks! tksurfer avoss_01 lh defect_labels subject is avoss_01 hemi is lh surface is defect_labels surfer: current subjects dir: /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf checking for nofix files in 'defect_labels' Reading image info (/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01) Reading /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz surfer: Reading header info from /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz nquads=4063237, nvertices=664 ERROR: MRISread: file '/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf/lh.defect_labels' has many more faces than vertices! Probably trying to use a scalar data file as a surface! No such file or directory #@# Fix Topology Copy lh Mon May 31 11:15:08 CEST 2021 /mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated # #@# Fix Topology Copy rh Mon May 31 11:15:08 CEST 2021 /mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Mon May 31 11:15:08 CEST 2021 mris_fix_topology -rusage /mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 avoss_01 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 * Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations :10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices :0 ordering dependant retessellation: 0 use precomputed edge table :0 smooth retessellated patch :2 match retessellated patch : 1 verbose mode : 0 * INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-236 (nv=170046, nf=340564, ne=510846, g=119) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 31240 ambiguous faces found in tessellation segmenting defects... 66 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 18 into 11 -merging segment 21 into 15 -merging segment 45 into 44 63 defects to be corrected 0 vertices coincident reading input surface /mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1568 (-4.5784) -vertex loglikelihood: -6.1795 (-3.0897) -normal dot loglikelihood: -3.5667 (-3.5667) -quad curv loglikelihood: -5.9168 (-2.9584) Total Loglikelihood : -24.8197 CORRECTING DEFECT 0 (vertices=65, convex hull=66, v0=6)
Re: [Freesurfer] Abormally high foldind index
External Email - Use Caution Hi Bruce, I looked at the pial surfaces and WM by running this for the outlier subjects: freeview -v subject1/mri/T1.mgz \ subject1/mri/brainmask.mgz \ -f subject1/surf/lh.white:edgecolor=yellow \ subject1/surf/lh.pial:edgecolor=red \ subject1/surf/rh.white:edgecolor=yellow \ subject1/surf/rh.pial:edgecolor=red Nothing stood out to me. Is there anything else you suggest I investigate? What could explain a negative folding index? Best, Ellen On 3/31/2021 12:18 AM, Fischl, Bruce wrote: > Hi Ellen > > It is certainly possible. Have you looked at the surfaces for those subjects? > > Cheers > Bruce > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > On Behalf Of Ellen Ji > Sent: Tuesday, March 30, 2021 5:44 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Abormally high foldind index > > External Email - Use Caution > > Dear Experts, > > While the majority of our subjects have a folding index between 5-30, there > are a couple of *extreme* outliers in the thousands or even negative. > > Could this hint that a particular part of recon-all failed and should be > rerun? > > Thank you for your interpretation and advice! > > -Ellen > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1lJSmdFC6cNktGONLnhAlvD7TBg-h0V1UpdjPaBc69QkV2k_Ftbva-AHPfz2nar2HSV4DE5N_AjKtmOrq8XmmT02qEcFGdzDZL1x-GubL8_3ya1rQpjOMDGU84wku_yR4svfjDl5adu54wg1sQ5th205CpcxlLr9iSeFKaSpsvr7pho0qBzXVwC4XlmxiH5LNWhX43zib-VJ7Mr-bW9V9ppd-SPmpku_6426YUSHSdKGVDd9A2lLYMsb6wWsn5SXE2ALmWhBulHZVlRcX3lIKdg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1lJSmdFC6cNktGONLnhAlvD7TBg-h0V1UpdjPaBc69QkV2k_Ftbva-AHPfz2nar2HSV4DE5N_AjKtmOrq8XmmT02qEcFGdzDZL1x-GubL8_3ya1rQpjOMDGU84wku_yR4svfjDl5adu54wg1sQ5th205CpcxlLr9iSeFKaSpsvr7pho0qBzXVwC4XlmxiH5LNWhX43zib-VJ7Mr-bW9V9ppd-SPmpku_6426YUSHSdKGVDd9A2lLYMsb6wWsn5SXE2ALmWhBulHZVlRcX3lIKdg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Abormally high foldind index
External Email - Use Caution Dear Experts, While the majority of our subjects have a folding index between 5-30, there are a couple of *extreme* outliers in the thousands or even negative. Could this hint that a particular part of recon-all failed and should be rerun? Thank you for your interpretation and advice! -Ellen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] left-right flip?
External Email - Use Caution
Thanks for your reply Doug. Yes, I'm thankful I figured it out with your
help!
In the meantime I already tried to run mri_convert based on the mri_info
--orientation information.
For instance, if mri_info --orientation yielded "LAS" for the nifti, I
performed mri_convert --in_orientation RAS inputfile.nii outputfile.nii.
Would this also yield the same output as the --left-right-reverse-pix
option you proposed?
Best,
Ellen
On 9/18/2020 4:54 PM, Douglas Greve wrote:
I'm sorry to hear it, but at least you figured it out. You're best
option is just to convert directly from the dicoms if you have them
using mri_convert, dcmunpack, or just passing a dicom file directly to
recon-all as input. If you don't have access to the dicoms, you can run
mri_convert inputfile.nii.gz --left-right-reverse-pix outputfile.nii.gz
On 9/16/20 12:03 PM, Fischl, Bruce wrote:
I think so, but I defer to Doug
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Ellen Ji
*Sent:* Wednesday, September 16, 2020 11:05 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] left-right flip?
*External Email - Use Caution *
Thanks for your reply Bruce. Could you confirm if I can run
mri_convert on the incorrectly flipped niftis to appropriately
correct them?
(https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal)
Something like:
mri_convert --in_orientation LIA subject1.nii subject1_corrected.nii
best,
Ellen
On 9/16/2020 4:47 PM, Fischl, Bruce wrote:
Hi Ellen
Sorry to say it, but you really should start over. Not everything in the
brain is bilaterally symmetric so processing and flipping won't be the same as
flipping then processing.
Cheers
Bruce
-Original Message-
From:freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Ellen Ji
Sent: Wednesday, September 16, 2020 3:41 AM
To:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] left-right flip?
External Email - Use Caution
Hi Douglas,
I found the dicoms and confirm that the fiducial is on the opposite side
relative to the nifti. Additionally, the PI just informed me that the fiducial
was placed on the right side of the head and the nifti indicates left. I will
enquire as to what method was used to convert from dicom as that appears to be
the issue.
I already performed recon-all and aparcstats2table on the flipped nifti.
Could you please advise if there is there an efficient way to deal with
this or if I should start from the beginning?
Many thanks,
Ellen
On 9/15/2020 7:19 PM, Douglas N. Greve wrote:
First we have to determine whether it is really LR flipped or not. Do
you still have the dicoms? If so, can you convert to mgz using
mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see
if the fiducial has changed sides relative to the nifti.
That is a fiducial. And do you know what side the fiducial was placed
on? mri_info does not help. How did you convert from dicom?
ps. Please make sure to post to the list and not to us personally
On 9/15/2020 12:58 PM, Ellen Ji wrote:
External Email - Use Caution
group cc'd - thanks for the reminder.
My input data was the niftis. Example: recon-all -i 1kl5011.nii
-subjid
1kl5011 -all
Is there an efficient way to handle the flipped L-R or should I
mri_convert the nifti and then do recon-all?
(Assuming that I can't just switch lh_ and rh_ in the
aparcstats2table)
Ellen
On 9/15/2020 6:51 PM, Fischl, Bruce wrote:
Hi Ellen
Can you cc the list so that others can respond? What was your
input data? Did you not have dicoms?
Cheers
Bruce
-Original Message-
From: Ellen Ji
<mailto:ellen...@bli.uzh.ch>
Sent: Tuesday, September 15, 2020 12:38 PM
To: Fischl, Bruce
<mailto:bfis...@mgh.harvard.edu>
Subject: Re: [Freesurfer] left-right flip?
External Email - Use Caution
Hi Bruce,
Unfortunately I just found the fiducial and realised that the
L-R is incorrect. Can I simply switch the lh_ and rh_ output from
aparcstats2table or do I need to run mri_convert on the nifti and run recon-all
from the beginning again?
Thanks,
Ellen
On 9/15/2020 5:44 PM, Fischl, Bruce wrote:
And what is your input to recon-all? If it is dicom you
should
Re: [Freesurfer] left-right flip?
External Email - Use Caution Thanks for your reply Bruce. Could you confirm if I can run mri_convert on the incorrectly flipped niftis to appropriately correct them? (https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal) Something like: mri_convert --in_orientation LIA subject1.nii subject1_corrected.nii best, Ellen On 9/16/2020 4:47 PM, Fischl, Bruce wrote: Hi Ellen Sorry to say it, but you really should start over. Not everything in the brain is bilaterally symmetric so processing and flipping won't be the same as flipping then processing. Cheers Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ellen Ji Sent: Wednesday, September 16, 2020 3:41 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip? External Email - Use Caution Hi Douglas, I found the dicoms and confirm that the fiducial is on the opposite side relative to the nifti. Additionally, the PI just informed me that the fiducial was placed on the right side of the head and the nifti indicates left. I will enquire as to what method was used to convert from dicom as that appears to be the issue. I already performed recon-all and aparcstats2table on the flipped nifti. Could you please advise if there is there an efficient way to deal with this or if I should start from the beginning? Many thanks, Ellen On 9/15/2020 7:19 PM, Douglas N. Greve wrote: First we have to determine whether it is really LR flipped or not. Do you still have the dicoms? If so, can you convert to mgz using mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see if the fiducial has changed sides relative to the nifti. That is a fiducial. And do you know what side the fiducial was placed on? mri_info does not help. How did you convert from dicom? ps. Please make sure to post to the list and not to us personally On 9/15/2020 12:58 PM, Ellen Ji wrote: External Email - Use Caution group cc'd - thanks for the reminder. My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid 1kl5011 -all Is there an efficient way to handle the flipped L-R or should I mri_convert the nifti and then do recon-all? (Assuming that I can't just switch lh_ and rh_ in the aparcstats2table) Ellen On 9/15/2020 6:51 PM, Fischl, Bruce wrote: Hi Ellen Can you cc the list so that others can respond? What was your input data? Did you not have dicoms? Cheers Bruce -Original Message- From: Ellen Ji Sent: Tuesday, September 15, 2020 12:38 PM To: Fischl, Bruce Subject: Re: [Freesurfer] left-right flip? External Email - Use Caution Hi Bruce, Unfortunately I just found the fiducial and realised that the L-R is incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table or do I need to run mri_convert on the nifti and run recon-all from the beginning again? Thanks, Ellen On 9/15/2020 5:44 PM, Fischl, Bruce wrote: And what is your input to recon-all? If it is dicom you should be pretty confident that we will get it correct -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 10:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip? How are you checking the LR orientation? On 9/15/2020 4:10 AM, Ellen Ji wrote: External Email - Use Caution Dear experts, I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts. For example, in our dataset, the lateral ventricle volume is on average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical. In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are. Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake! I found this website on Left-right reversal, and it seems relevant to my issue, but I'm not fully understanding what this means (how would bias occur during segmentation?) - https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal Many thanks for your input, Ellen --- Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen...@bli.uzh.ch homanlab.github.io/ellen/ ___ Freesurfer mailing list Freesurfer
Re: [Freesurfer] left-right flip?
External Email - Use Caution Hi Douglas, I found the dicoms and confirm that the fiducial is on the opposite side relative to the nifti. Additionally, the PI just informed me that the fiducial was placed on the right side of the head and the nifti indicates left. I will enquire as to what method was used to convert from dicom as that appears to be the issue. I already performed recon-all and aparcstats2table on the flipped nifti. Could you please advise if there is there an efficient way to deal with this or if I should start from the beginning? Many thanks, Ellen On 9/15/2020 7:19 PM, Douglas N. Greve wrote: > First we have to determine whether it is really LR flipped or not. Do > you still have the dicoms? If so, can you convert to mgz using > mri_convert one-dicom-file.dcm test.mgz > Then look at test.mgz and see if the fiducial has changed sides relative > to the nifti. > That is a fiducial. And do you know what side the fiducial was placed > on? mri_info does not help. How did you convert from dicom? > > ps. Please make sure to post to the list and not to us personally > > > On 9/15/2020 12:58 PM, Ellen Ji wrote: >> External Email - Use Caution >> >> group cc'd - thanks for the reminder. >> >> My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid >> 1kl5011 -all >> >> Is there an efficient way to handle the flipped L-R or should I >> mri_convert the nifti and then do recon-all? >> >> (Assuming that I can't just switch lh_ and rh_ in the aparcstats2table) >> >> Ellen >> >> On 9/15/2020 6:51 PM, Fischl, Bruce wrote: >>> Hi Ellen >>> >>> Can you cc the list so that others can respond? What was your input data? >>> Did you not have dicoms? >>> >>> Cheers >>> Bruce >>> >>> -Original Message- >>> From: Ellen Ji >>> Sent: Tuesday, September 15, 2020 12:38 PM >>> To: Fischl, Bruce >>> Subject: Re: [Freesurfer] left-right flip? >>> >>>External Email - Use Caution >>> >>> Hi Bruce, >>> >>> Unfortunately I just found the fiducial and realised that the L-R is >>> incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table >>> or do I need to run mri_convert on the nifti and run recon-all from the >>> beginning again? >>> >>> Thanks, >>> >>> Ellen >>> >>> On 9/15/2020 5:44 PM, Fischl, Bruce wrote: >>>> And what is your input to recon-all? If it is dicom you should be >>>> pretty confident that we will get it correct >>>> >>>> -Original Message- >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>> On Behalf Of Douglas N. Greve >>>> Sent: Tuesday, September 15, 2020 10:17 AM >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] left-right flip? >>>> >>>> How are you checking the LR orientation? >>>> >>>> On 9/15/2020 4:10 AM, Ellen Ji wrote: >>>>> External Email - Use Caution >>>>> >>>>> Dear experts, >>>>> >>>>> I recently performed recon-all on a set of subjects and the output >>>>> (aparcstats2table and asegstats2table) will be part of a meta-analysis of >>>>> other labs' cohorts. When assessing the asymmetry index direction >>>>> (relative size of left vs right hemisphere across multiple rois), our >>>>> dataset shows an inversion of the mean asymmetry index in several >>>>> structures compared to the other cohorts. >>>>> >>>>> For example, in our dataset, the lateral ventricle volume is on >>>>> average larger in the right hemisphere compared to the left, while the >>>>> opposite is true for all other cohorts. The same inversion of asymmetry >>>>> is visible in other structures that in general are more asymmetrical. >>>>> >>>>> In order to check this, I went through each T1 to make sure the >>>>> orientation was correct and indeed they are. >>>>> >>>>> Is there any possible way that there was a left-right inversion somewhere >>>>> during the recon-all pipeline? I want to make sure I did everything >>>>> correctly on our end and that the results are due to the biology and not >>>>> a technical mistake! >>>>> >>>
Re: [Freesurfer] left-right flip?
External Email - Use Caution group cc'd - thanks for the reminder. My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid 1kl5011 -all Is there an efficient way to handle the flipped L-R or should I mri_convert the nifti and then do recon-all? (Assuming that I can't just switch lh_ and rh_ in the aparcstats2table) Ellen On 9/15/2020 6:51 PM, Fischl, Bruce wrote: > Hi Ellen > > Can you cc the list so that others can respond? What was your input data? Did > you not have dicoms? > > Cheers > Bruce > > -Original Message- > From: Ellen Ji > Sent: Tuesday, September 15, 2020 12:38 PM > To: Fischl, Bruce > Subject: Re: [Freesurfer] left-right flip? > > External Email - Use Caution > > Hi Bruce, > > Unfortunately I just found the fiducial and realised that the L-R is > incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table > or do I need to run mri_convert on the nifti and run recon-all from the > beginning again? > > Thanks, > > Ellen > > On 9/15/2020 5:44 PM, Fischl, Bruce wrote: >> And what is your input to recon-all? If it is dicom you should be >> pretty confident that we will get it correct >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> On Behalf Of Douglas N. Greve >> Sent: Tuesday, September 15, 2020 10:17 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] left-right flip? >> >> How are you checking the LR orientation? >> >> On 9/15/2020 4:10 AM, Ellen Ji wrote: >>>External Email - Use Caution >>> >>> Dear experts, >>> >>> I recently performed recon-all on a set of subjects and the output >>> (aparcstats2table and asegstats2table) will be part of a meta-analysis of >>> other labs' cohorts. When assessing the asymmetry index direction (relative >>> size of left vs right hemisphere across multiple rois), our dataset shows >>> an inversion of the mean asymmetry index in several structures compared to >>> the other cohorts. >>> >>> For example, in our dataset, the lateral ventricle volume is on >>> average larger in the right hemisphere compared to the left, while the >>> opposite is true for all other cohorts. The same inversion of asymmetry is >>> visible in other structures that in general are more asymmetrical. >>> >>> In order to check this, I went through each T1 to make sure the orientation >>> was correct and indeed they are. >>> >>> Is there any possible way that there was a left-right inversion somewhere >>> during the recon-all pipeline? I want to make sure I did everything >>> correctly on our end and that the results are due to the biology and not a >>> technical mistake! >>> >>> I found this website on Left-right reversal, and it seems relevant to >>> my issue, but I'm not fully understanding what this means (how would >>> bias occur during segmentation?) - >>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal >>> >>> Many thanks for your input, >>> Ellen >>> >>> --- >>> >>> Ellen Ji, PhD >>> Postdoctoral Research Fellow >>> Psychiatric University Hospital >>> University of Zürich >>> ellen...@bli.uzh.ch >>> homanlab.github.io/ellen/ >>> >>> >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> ___ >> Freesurfer mailing list >> Freesurfer@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 Mass General Brigham > Compliance HelpLine at http://www.massgeneralbrigham.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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] left-right flip?
External Email - Use Caution Dear experts, I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts. For example, in our dataset, the lateral ventricle volume is on average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical. In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are. Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake! I found this website on Left-right reversal, and it seems relevant to my issue, but I'm not fully understanding what this means (how would bias occur during segmentation?) - https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal Many thanks for your input, Ellen --- Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen...@bli.uzh.ch homanlab.github.io/ellen/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Permission denied mri_surf2surf
External Email - Use Caution Dear experts, I created a loop for mri_surf2surf so that it would run for 300+ subjects. For most of them, it ran successfully. However, it did not work for 30 subjects. I then went to investigate one by one and I am getting a Permission denied error for some reason. I confirm that recon-all has been performed and also that I have read/write/execute permissions. See below for the log. Any ideas why this could be happening to specific subjects? mri_surf2surf \ --srcsubject fsaverage_sym \ --trgsubject SPN01_CMH_0079_01 \ --hemi lh \ --sval-annot fsaverage_sym/label/lh.500_sym.aparc.annot \ --tval SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot Setting mapmethod to nnf 7.1.0 setenv SUBJECTS_DIR /home/eji/projects/spins/preproc/freesurfer/subjects/w0 cd /home/eji/projects/spins/preproc/freesurfer/subjects/w0 mri_surf2surf --srcsubject fsaverage_sym --trgsubject SPN01_CMH_0079_01 --hemi lh --sval-annot fsaverage_sym/label/lh.500_sym.aparc.annot --tval SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot sysname Linux hostname nu2 machine x86_64 user eji srcsubject = fsaverage_sym srcval = (null) srctype = trgsubject = SPN01_CMH_0079_01 trgval = SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/eji/projects/spins/preproc/freesurfer/subjects/w0/fsaverage_sym/surf/lh.sphere.reg Loading source data Reading surface file /home/eji/projects/spins/preproc/freesurfer/subjects/w0/fsaverage_sym/surf/lh.orig reading colortable from annotation file... colortable with 161 entries read (originally /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab) Reading target surface reg /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0079_01/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (123600) Surf2Surf: Dividing by number of hits (123600) INFO: nSrcLost = 61776 nTrg121 = 123600, nTrgMulti = 0, MnTrgMultiHits = 0 nSrc121 = 85136, nSrcLost = 61776, nSrcMulti = 78706, MnSrcMultiHits = 0.488705 Saving target data Converting to target annot Saving to target annot SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot error: Permission denied error: could not write annot file SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_aparc2aseg: how to remove redundant output labels?
External Email - Use Caution
Dear experts,
I am running mri_aparc2aseg using two annotations as input (one for each
hemisphere), each with 159 labels, and wish to end up with a single
output segmentation of 318 labels. However, when I run the below, this
is not the case:
mri_aparc2aseg \
--s subject1 \
--annot 500_sym.aparc \
--wmparc-dmax 2 \
--labelwm \
--hypo-as-wm \
--o subject1/mri/parcellation.nii.gz
In fact, the output has 680 labels rather than 318 labels. A few questions.
- How can I see what exactly the 680 label names are (how to extract
from the .nii.gz output file)? Currently, I have just quantified it to
be 680 by doing this in matlab: gunzip('parcellation.nii.gz')
a = MRIread('parcellation.nii');
u = unique(a.vol(:));
length(u) % total number of labels
- I believe the extra labels are from the Freesurfer LUT. How can I make
sure they are not added when running mri_aparc2aseg? (such that only my
annotation labels are included in the output)
Thank you very much,
Ellen
*
Ellen Ji, PhD
Postdoctoral Research Fellow
Psychiatric University Hospital
University of Zürich
ellen...@bli.uzh.ch
homanlab.github.io/ellen/
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] mri_aparc2aseg doesn't write output
External Email - Use Caution Dear experts, I am running mri_aparc2aseg and, based on the output, it seems to run through successfully until the very end where it does not actually write the file (I receive "error: niiWrite(): error opening file mri/aparc.500+2mm.nii.gz"). However, I am 100% sure that I have writing access in the directory. Below you will see the details. Do you know why I am having this issue? Thank you for your time, Ellen mri_aparc2aseg \ --s SPN01_CMH_0001_01 \ --annot 500_sym.aparc \ --wmparc-dmax 2 \ --labelwm \ --hypo-as-wm \ --o mri/aparc.500+2mm.nii.gz SUBJECTS_DIR /home/eji/projects/spins/preproc/freesurfer/subjects/w0 subject SPN01_CMH_0001_01 outvol mri/aparc.500+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.00 RipUnknown 0 8 avail.processors, using 1 Reading lh white surface /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/surf/lh.white Reading lh pial surface /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/surf/lh.pial Loading lh annotations from /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/label/lh.500_sym.aparc.annot reading colortable from annotation file... colortable with 161 entries read (originally /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab) Have color table for lh white annotation Building hash of lh white Building hash of lh pial Reading rh white surface /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/surf/rh.white Reading rh pial surface /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/surf/rh.pial Loading rh annotations from /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/label/rh.500_sym.aparc.annot reading colortable from annotation file... colortable with 161 entries read (originally /scratch/tmpdir.annot2std.12874/seg.1.073.xhemi.ctab) Have color table for rh white annotation Building hash of rh white Building hash of rh pial Loading ribbon segmentation from /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/mri/ribbon.mgz Loading filled from /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/mri/ribbon.mgz Loading aseg from /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/mri/aseg.mgz ASeg Vox2RAS: --- -1.0 0.0 0.0 128.0; 0.0 0.0 1.0 -128.0; 0.0 -1.0 0.0 128.0; 0.0 0.0 0.0 1.0; - Labeling Slice (256) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 906029 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 1 clusters 0 k 791.00 Fixing Parahip RH WM Found 3 clusters 0 k 751.00 1 k 1.00 2 k 2.00 Writing output aseg to mri/aparc.500+2mm.nii.gz error: niiWrite(): error opening file mri/aparc.500+2mm.nii.gz #VMPC# mri_aparc2aseg VmPeak 1376092 mri_aparc2aseg done ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] bbregister using freesurfer v7
External Email - Use Caution Dear experts, I am running bbregister and have a couple questions: 1) I am using freesurfer version 7. My understanding is that I do not need any --init argument anymore, and without it, by default it uses init-coreg. Could you confirm this? (I tested the below and it seemed fine) bbregister --s subject1 --mov $dtipath/subject1/data.nii.gz --dti --reg mri/register.dat 2) A colleague performed recon-all using freesurfer v6. Is it ok if I use bbregister on these subjects using freesurfer v7 or should I install v6? Many thanks for your input! Ellen Ji, PhD Postdoctoral researcher * Individual Differences in Psychosis (IDP) Lab Psychiatric University Hospital University of Zürich ellen...@bli.uzh.ch ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
