Re: [Freesurfer] Ventricle Volumes Decreasing over time?
Hi Bruce, Thank you for your quick reply! The decrease in percent difference vary. I have listed the range here for each region: Left Lateral Ventricle: -26 to -0.06 Left inferior ventricles: -67 to -0.2 Third ventricle: -23 to -0.06 Fourth ventricle: -7 to -0.142 Right lateral ventricle: -21 to -0.04 Right inferior ventricle: -59 to -0.68 I had a chance to examine one brain that showed -16% difference score in the left lateral ventricles between the longitudinal and baseline scan. The scans seemed to show a smaller left lateral ventricle at time 2. Do you know whether the variability of Freesurfer (version 5.1) may contribute to some of the decreases I am seeing? Thank you in advance for your help. Best, Tamara Message: 32 Date: Tue, 5 Sep 2017 21:43:23 -0400 (EDT) From: Bruce Fischl Subject: Re: [Freesurfer] Ventricle Volumes Decreasing over time? To: Freesurfer support list Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Tamara have you visualized the multiple time points of a subject whose ventricular volume is decreasing? How big a decrease are you seeing? cheers Bruce On Tue, 5 Sep 2017, Tamara Tavares wrote: > Hello, > I used the default longitudinal stream to calculate ventricular volumes over time. When I examined > the difference score (longitudinal-baseline) I noticed that for some participants ventricular > volumes decreased. The same site, scanner and scanning protocol was used for both baseline and > longitudinal scans. I processed the cross, template and longitudinal time points on the same > computer using the same Freesurfer version (v 5.1). Furthermore, this decrease in ventricular volume > is evident before and after manual corrects were made to the aseg file. Is it common to see an > decrease in ventricular volume over time? Can this be due to Freesurfer variability or slight > differences in the scanner over the two time points? > > Thank you in advance for your help. > > Best, > Tamara ___ 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 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.
Re: [Freesurfer] rh.white and rh.pial surface manual edit
Hi Farhad, I'd be happy to help you with this problem. This appears to be a topological defect. You can edit the white matter volume (wm.mgz) by using the recon edit button to remove the section of white matter that is connecting the gyri. After making the edits and saving the volume, you can re-run recon all with the following command: recon-all -autorecon2-wm -autorecon3 -subjid . By editing the white matter volume, both the white matter and pial surfaces will be regenerated. I recommend looking at the following link for additional information. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview If you have any further questions, feel free to ask. Morgan From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Farhad Ghaseminejad [a.farha...@gmail.com] Sent: Thursday, August 31, 2017 1:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] rh.white and rh.pial surface manual edit Hello FreeSurfer experts, I was wondering if you have any suggestions on how to fix the error in the rh.white and rh.pial surface in the Orbitofrontal cortex as shown in the screenshots attached. https://drive.google.com/drive/folders/0B64fNVlVdTBYOVhJMXJyTjZVSTQ?usp=sharing Best, Farhad ___ 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 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.
Re: [Freesurfer] Error while running recon-all
Hi Ritesh, What operating system and version are you running freesurfer on, ubuntu? Can you also send the fs version build stamp (you can get this by running 'bugr’) best Andrew > On Aug 29, 2017, at 11:41 AM, Ritesh Mahajan > wrote: > > Hello guys, > > I am trying to run recon-all command, i am getting the following error: > > error while loading shared libraries: libgomp.so.1: cannot open shared object > file: No such file or directory > > Can anyone help me out with this. > > Thanks, > Ritesh Mahajan > ___ > 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 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.
Re: [Freesurfer] Philips and Toshiba dicom tag Read - error
yes, it looked like it worked fine. Have you visualized the results? cheers Bruce On Wed, 6 Sep 2017, M Janani wrote: Hi Team, We would like to process the MRI data obtained using Philips and Toshiba scanners. Can we do it using Freesurfer? Thought the reconstruction process got completed successfully, we got DICOM read error while fetching DWI parameters in the beginning of the reconstruction process. Can I neglect that error? Attached log for reference. Regards, Janani ::DISCLAIMER:: --- - The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. --- - ___ 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 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.
Re: [Freesurfer] wm topological defects
Hi Ilona yes, you only need to edit the wm in regions where inaccuracies in the wm.mgz are making the surfaces inaccurate cheers Bruce On Wed, 6 Sep 2017, Ruotsalainen, Ilona wrote: Dear experts, I would have a follow up question for this thread. I have erased voxels from areas which are not white matter, but classified as white matter in wm.mgz (such as blood vessels and tissue outside brain that clearly are not white matter) or filled "holes" in wm.mgz (example in pictures hole_wm1 and hole_wm2). I have done this even the surfaces look accurate. After checking the aparc.stats-file there are sometimes quite large changes in volumes of specific areas (even over 10%). So my question is following. Should I only fix those parts in wm.mgz in which the ?h.pial and/or ?h.white are not accurate and leave other parts of wm.mgz unfixed even the mask clearly includes regions that are not white matter? I have read the tutorials, but I'm still not certain about this issue. Thank you, Ilona Ruotsalainen -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: tiistai 4. heinäkuuta 2017 20:43 To: Freesurfer support list Subject: Re: [Freesurfer] wm topological defects Hi Manuel you should examine the ?h.white and ?h.pial for accuracy, and only use the .nofix surfaces if you are trying to figure out why the white/pial are not as accurate as you would like Bruce On Tue, 4 Jul 2017, Manuel Delgado wrote: Dear all: Regarding wm edits, it is shown in the tutorial how to proceed with "holes" that appear in the smoothwm.nofix. However, those holes do not necessarily affect the wm matter surface. So is it recommendable to check if holes in the smoothwm.nofix surface affect the real wm surface before correcting them? And, what is the purpose of the smoothwm.nofix, is it used for other issues? Thank you -- Manuel Delgado Alvarado, MD Predoctoral Researcher Neuroimaging Unit, IDIVAL [LogoIDIVAL.PNG?ver=2015-10-14-180234-000] Avda. Cardenal Herrera Oria s/n 39011 Santander, Spain ___ 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 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. ___ 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 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.
[Freesurfer] Cortical Parcellation Yeo2011
Hi list, I have already run by recon-all -all all my subjects in order to run PetSurfer. Output stats is saved in gtm.stats.dat and values correspond to Desikan-Killiany Atlas, However, I am interested in calculating values using Yeo atlas of 7 networks. Do you have any suggestions to get Partial Volume Corrected values from Yeo atlas for each subject? Do I have to switch to Yao atlas during recon-all -all process or during gtmseg? Thank you Lorenzo ___ 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 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.
Re: [Freesurfer] Ventricle Volumes Decreasing over time?
Hi Tamara but have you looked at the two timepoints in freeview to see if the ventricles are actually decreasing or of it is a segmentation error? Is that what you mean when you say you examined it? If the segmentations look accurate I'm not sure what else we can do. I guess you could try installing 6.0 and rerunning these subjects to see if the results persist. 5.1 is pretty old cheers Bruce On Wed, 6 Sep 2017, Tamara Tavares wrote: Hi Bruce, Thank you for your quick reply! The decrease in percent difference vary. I have listed the range here for each region: Left Lateral Ventricle: -26 to -0.06 Left inferior ventricles: -67 to -0.2 Third ventricle: -23 to -0.06 Fourth ventricle: -7 to -0.142 Right lateral ventricle: -21 to -0.04 Right inferior ventricle: -59 to -0.68 I had a chance to examine one brain that showed -16% difference score in the left lateral ventricles between the longitudinal and baseline scan. The scans seemed to show a smaller left lateral ventricle at time 2. Do you know whether the variability of Freesurfer (version 5.1) may contribute to some of the decreases I am seeing? Thank you in advance for your help. Best, Tamara Message: 32 Date: Tue, 5 Sep 2017 21:43:23 -0400 (EDT) From: Bruce Fischl Subject: Re: [Freesurfer] Ventricle Volumes Decreasing over time? To: Freesurfer support list Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Tamara have you visualized the multiple time points of a subject whose ventricular volume is decreasing? How big a decrease are you seeing? cheers Bruce On Tue, 5 Sep 2017, Tamara Tavares wrote: > Hello, > I used the default longitudinal stream to calculate ventricular volumes over time. When I examined > the difference score (longitudinal-baseline) I noticed that for some participants ventricular > volumes decreased. The same site, scanner and scanning protocol was used for both baseline and > longitudinal scans. I processed the cross, template and longitudinal time points on the same > computer using the same Freesurfer version (v 5.1). Furthermore, this decrease in ventricular volume > is evident before and after manual corrects were made to the aseg file. Is it common to see an > decrease in ventricular volume over time? Can this be due to Freesurfer variability or slight > differences in the scanner over the two time points? > > Thank you in advance for your help. > > Best, > Tamara ___ 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 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.
Re: [Freesurfer] wm topological defects
Thank you for your reply! Ilona Lähettäjä: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] käyttäjän Bruce Fischl [fis...@nmr.mgh.harvard.edu] puolesta Lähetetty: 6. syyskuuta 2017 16:56 Vastaanottaja: Freesurfer support list Aihe: Re: [Freesurfer] wm topological defects Hi Ilona yes, you only need to edit the wm in regions where inaccuracies in the wm.mgz are making the surfaces inaccurate cheers Bruce On Wed, 6 Sep 2017, Ruotsalainen, Ilona wrote: > Dear experts, > > I would have a follow up question for this thread. > > I have erased voxels from areas which are not white matter, but classified as > white matter in wm.mgz (such as blood vessels and tissue outside brain that > clearly are not white matter) or filled "holes" in wm.mgz (example in > pictures hole_wm1 and hole_wm2). I have done this even the surfaces look > accurate. After checking the aparc.stats-file there are sometimes quite > large changes in volumes of specific areas (even over 10%). So my question is > following. Should I only fix those parts in wm.mgz in which the ?h.pial > and/or ?h.white are not accurate and leave other parts of wm.mgz unfixed even > the mask clearly includes regions that are not white matter? I have read the > tutorials, but I'm still not certain about this issue. > > Thank you, > Ilona Ruotsalainen > > > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: tiistai 4. heinäkuuta 2017 20:43 > To: Freesurfer support list > Subject: Re: [Freesurfer] wm topological defects > > Hi Manuel > > you should examine the ?h.white and ?h.pial for accuracy, and only use the > .nofix surfaces if you are trying to figure out why the white/pial are not as > accurate as you would like Bruce > > > On Tue, 4 Jul 2017, Manuel Delgado wrote: > >> Dear all: >> Regarding wm edits, it is shown in the tutorial how to proceed with "holes" >> that appear in the smoothwm.nofix. However, those holes do not >> necessarily affect the wm matter surface. So is it recommendable to >> check if holes in the smoothwm.nofix surface affect the real wm >> surface before correcting them? And, what is the purpose of the >> smoothwm.nofix, is it used for other issues? >> Thank you >> >> -- >> Manuel Delgado Alvarado, MD >> >> Predoctoral Researcher >> Neuroimaging Unit, IDIVAL >> [LogoIDIVAL.PNG?ver=2015-10-14-180234-000] >> Avda. Cardenal Herrera Oria s/n >> 39011 Santander, Spain >> >> >> > ___ > 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 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. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] patch for ribbon mgz failure. SAME ERROR
what happens if you run recon-all -s subject -cortribbon does it create the ribbon.mgz? On 9/6/17 7:53 AM, Maria Gloria Rossetti wrote: Hi Doug, As you suggested, I copied the mri_segstats patch (mri_segstats.centos6_x86_64 because my system is centos6) to my freesurfer/bin location and reran the pipeline. However, I'm getting the same issue. Autorecon2 seems unable to create the ribbon.mgz file. Do you have any other suggestions for fixing this error? Attached you can find the recon-all.log file Thanks, Gloria *Da: *"Douglas N Greve" *A: *"freesurfer" *Inviato: *Martedì, 5 settembre 2017 18:09:31 *Oggetto: *Re: [Freesurfer] patch for ribbon mgz failure Use the mri_segstats from this URL that is appropriate for your system (eg, if you're running centos6, the download that patch and copy it to mri_segstats) https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ On 08/30/2017 06:32 AM, Maria Gloria Rossetti wrote: > Hi freesurfer team, > > I got the same error described here: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45983.html > and, as suggested, I tried to copy in $FREESURFER_HOME/bin/ the patch > from > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats > but I cannot find the URL. > I also found some patches here : > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ > but I don't know which one I'm supposed to use. > > Any advice? > > Thanks! > Gloria > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ 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 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. ___ 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 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.
Re: [Freesurfer] 答复: ROI
Hi Bo have you tried freeview? We don't support tksurfer any more. cheers Bruce On Wed, 6 Sep 2017, Jin Bo wrote: Hi all, I am a new to Freesurfer. I am currently useing freeview to get ROI(small lesion) on 7T MRI, but the ROI can not display on surface(tksurfer patient lh inflated -overlay patient/label/fcd.label ). The terminal showed the following sentence: label stat field identically zero - setting to 1 However, it works well on 3T MRI. Thanks, Bo 发件人: Jin Bo 发送时间: 2017年9月6日 8:11:40 收件人: freesurfer@nmr.mgh.harvard.edu 主题: ROI Hi all, I am a new to Freesurfer. I am currently useing freeview to get ROI(small lesion) on 7T MRI, but the ROI can not display on surface(tksurfer patient lh inflated -overlay patient/label/fcd.label ). The terminal showed the following sentence: label stat field identically zero - setting to 1 However, it works well on 3T MRI. Thanks, Bo ___ 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 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.
Re: [Freesurfer] Error while running recon-all
Thanks Andrew for your response. There were few libraries missing on OS level, i resolved the problem. Thanks, Ritesh Mahajan - Original Message - From: "Hoopes, Andrew" To: "freesurfer" Sent: Wednesday, September 6, 2017 7:24:03 PM Subject: Re: [Freesurfer] Error while running recon-all Hi Ritesh, What operating system and version are you running freesurfer on, ubuntu? Can you also send the fs version build stamp (you can get this by running 'bugr’) best Andrew > On Aug 29, 2017, at 11:41 AM, Ritesh Mahajan > wrote: > > Hello guys, > > I am trying to run recon-all command, i am getting the following error: > > error while loading shared libraries: libgomp.so.1: cannot open shared object > file: No such file or directory > > Can anyone help me out with this. > > Thanks, > Ritesh Mahajan > ___ > 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 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
