Re: [Freesurfer] cannot find qdec file
no worries! sadly, though, deleting the empty line wasn't the answer to the problem :( Cheers, Clara - Ursprüngliche Mail - Von: Douglas N Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 4. August 2015 20:43:47 Betreff: Re: [Freesurfer] cannot find qdec file oops, sorry for the delay, thanks for the reminder. The problem is that you have a blank line at the end of your long.qdec.table.dat file. Remove the line and see if it works. doug On 08/04/2015 12:42 PM, Clara Kühn wrote: Hi Doug, did the fordoug.log file give any information about why FreeSurfer can't find my qdec file? Cheers and thanks for working on this! Clara - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 17:16:18 Betreff: Re: [Freesurfer] cannot find qdec file can you run mris_preproc --debug --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh | tee fordoug.log and send me fordoug.log ? On 8/3/15 10:38 AM, Clara Kühn wrote: the command line is this: mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh the terminal output is this: nsubjects = 22 ERROR: cannot find /scr/etsch2/kids/ct/.long. and the actual qdec file is attached. Cheers, Clara - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24 Betreff: Re: [Freesurfer] cannot find qdec file Can you send your command line, full terminal output, and your long.qdec.table.dat file? On 8/3/15 10:31 AM, Clara Kühn wrote: ok, it can only access the file if I type ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash) but if I then use that path for the mris_preproc command I get nsubjects = 22 ERROR: cannot find /scr/etsch2/kids/ct/.long. - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:23:48 Betreff: Re: [Freesurfer] cannot find qdec file that is probably not the full path. Try typing ls scr/etsch2/kids/ct/qdec/long.qdec.table.dat If it says it cannot find the file, then it is not the full path. Maybe you need a forward slash (ie, /) in the beginning? On 8/3/15 10:18 AM, Clara Kühn wrote: then I get the error ERROR: cannot find scr/etsch2/kids/ct/qdec/long.qdec.table.dat I had tried that. Sorry, no luck with that. - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:16:58 Betreff: Re: [Freesurfer] cannot find qdec file you have to give it the entire path to the file On 8/3/15 10:14 AM, Clara Kühn wrote: Dear FS-experts, I want to analyze my longitudinal data with your suggested LME models and am therefore following the walkthrough by J. Bernal. I get an error though very early on when using the command mris_preproc --qdec-long qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out qdec/lh.thickness.mgh It always says ERROR: cannot find qdec/long.qdec.table.dat Yes, the walkthrough asks for an input file named just qdec.table.dat, but I haven't got that. So far in the longitudinal stream there are long.qdec.table.dat and cross.qdec.table.dat files but no simple qdec.table.dat files. So I figured I'd use the long.qdec file because FS needs to get the information about the long timepoints. But it cannot find the file, even though I see it. I've also tried copying the long.qdec file and naming it qdec.table.dat but it still doesn't find it. The entire path to the file is scr/etsch2/kids/ct/qdec/long.qdec.table.dat and my SUBJECTS_DIR is scr/etsch2/kids/ct Can you help me see what I'm missing? Thanks a lot in advance, Clara ___ 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
Re: [Freesurfer] Repost: problem with mri_label2label - large amount of holes
Hi Bruce, Doug, and Zeke, just checking back regarding the dev version for mri_label2label. Do you have a build that works on MAC OS 10.9.5 Mavericks? So far, we have been using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0. Thank you, Caspar 2015-08-03 6:40 GMT-04:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu : We are using MAC OS 10.9.5 Mavericks and freesurfer-Darwin-leopard- i686-stable-pub-v5.1.0 On Thursday, July 30, 2015, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Caspar the dev version of label2label doesn't have this problem. If you let us know your hardware/software environment Zeke can get you a new binary that should fix this issue cheers Bruce On Thu, 30 Jul 2015, Caspar M. Schwiedrzik wrote: Hi Bruce and Doug, thanks for looking into this and sorry for the delay. The command line we are using is: mri_label2label --srclabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p 8.label --srcsubject y$1 --trglabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp 2.label --trgsubject yx$1 --regmethod surface --hemi lh We have several anatomies from the same subject, acquired on different occasions. We defined labels based on results of an fMRI experiment, and tried to use mri_label2label to map them within subjects from one anatomy to another. As a control, we also wanted to map the Hinds V1 from one anatomy to another, but this is where we ran into these holes. We will make an example subject available for debugging later today. Thanks! Caspar 2015-07-24 12:33 GMT-04:00 Douglas Greve gr...@nmr.mgh.harvard.edu: what is your command line? What do you mean by one anatomy to another? On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote: -- Forwarded message -- From: Caspar M. Schwiedrzik cschwie...@rockefeller.edu Date: Thursday, July 16, 2015 Subject: problem with mri_label2label - large amount of holes To: Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Hi! We are doing some analyses in which we map custom labels from one anatomy to another, within subjects. As a control, we also tried to map anatomically defined V1s according to the method by Hinds within subject from one anatomy to another. However, as you can see in the attachment, there are very many holes in the labels after using mri_label2label. This does not happen with smaller labels. Why is this happening and is there a solution? Thanks, Caspar ___ 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 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] registering NHP data
Awesome that you guys are working a parcellation! In the meantime, if I wanted to try to use the atlases you suggested, how would I go about processing the data? Is there documentation I can follow? Thanks so much, Mia From: MCLAREN, Donald [mclaren.don...@gmail.com] Sent: Tuesday, August 04, 2015 9:36 AM To: Borzello, Mia Subject: Re: [Freesurfer] registering NHP data Mia, You could use the 112RM-SL atlas for normalization and then use the Saleem-Logothetis Atlas for localization. Hopefully, by August, we'll have a parcellation on the the MR image so that localization can be done automatically. Best Regards, Donald McLaren, PhD On Mon, Aug 3, 2015 at 2:01 PM, Borzello, Mia mborze...@partners.orgmailto:mborze...@partners.org wrote: Hi Freesurfer experts, Does Freesurfer have a separate pipeline for registering NHP data? I am trying to register macaque data and localize the implanted electrodes, but the normal protocol errored. I did a google search and found this- is this what I should be using?: https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData I downloaded the scripts but I'm not sure what commands I'm supposed to be running, etc. Any guidance you can give would be must appreciated! Thanks, m ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
Re: [Freesurfer] Repost: problem with mri_label2label - large amount of holes
Hello Caspar, I did a quick test and it appears the new dev version of mri_label2label is still compatible with the version of 5.1 that you have. Please use the following link to download it and also please make sure to back up the version you already have. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/snowleopard-i686/mri_label2label -Zeke Hi Bruce, Doug, and Zeke, just checking back regarding the dev version for mri_label2label. Do you have a build that works on MAC OS 10.9.5 Mavericks? So far, we have been using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0. Thank you, Caspar 2015-08-03 6:40 GMT-04:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu : We are using MAC OS 10.9.5 Mavericks and freesurfer-Darwin-leopard- i686-stable-pub-v5.1.0 On Thursday, July 30, 2015, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Caspar the dev version of label2label doesn't have this problem. If you let us know your hardware/software environment Zeke can get you a new binary that should fix this issue cheers Bruce On Thu, 30 Jul 2015, Caspar M. Schwiedrzik wrote: Hi Bruce and Doug, thanks for looking into this and sorry for the delay. The command line we are using is: mri_label2label --srclabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p 8.label --srcsubject y$1 --trglabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp 2.label --trgsubject yx$1 --regmethod surface --hemi lh We have several anatomies from the same subject, acquired on different occasions. We defined labels based on results of an fMRI experiment, and tried to use mri_label2label to map them within subjects from one anatomy to another. As a control, we also wanted to map the Hinds V1 from one anatomy to another, but this is where we ran into these holes. We will make an example subject available for debugging later today. Thanks! Caspar 2015-07-24 12:33 GMT-04:00 Douglas Greve gr...@nmr.mgh.harvard.edu: what is your command line? What do you mean by one anatomy to another? On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote: -- Forwarded message -- From: Caspar M. Schwiedrzik cschwie...@rockefeller.edu Date: Thursday, July 16, 2015 Subject: problem with mri_label2label - large amount of holes To: Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Hi! We are doing some analyses in which we map custom labels from one anatomy to another, within subjects. As a control, we also tried to map anatomically defined V1s according to the method by Hinds within subject from one anatomy to another. However, as you can see in the attachment, there are very many holes in the labels after using mri_label2label. This does not happen with smaller labels. Why is this happening and is there a solution? Thanks, Caspar ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Repost: problem with mri_label2label - large amount of holes
Hi Zeke, Thank you, we will give it a try! Caspar On Wednesday, August 5, 2015, zkauf...@nmr.mgh.harvard.edu wrote: Hello Caspar, I did a quick test and it appears the new dev version of mri_label2label is still compatible with the version of 5.1 that you have. Please use the following link to download it and also please make sure to back up the version you already have. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/snowleopard-i686/mri_label2label -Zeke Hi Bruce, Doug, and Zeke, just checking back regarding the dev version for mri_label2label. Do you have a build that works on MAC OS 10.9.5 Mavericks? So far, we have been using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0. Thank you, Caspar 2015-08-03 6:40 GMT-04:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu javascript:; : We are using MAC OS 10.9.5 Mavericks and freesurfer-Darwin-leopard- i686-stable-pub-v5.1.0 On Thursday, July 30, 2015, Bruce Fischl fis...@nmr.mgh.harvard.edu javascript:; wrote: Hi Caspar the dev version of label2label doesn't have this problem. If you let us know your hardware/software environment Zeke can get you a new binary that should fix this issue cheers Bruce On Thu, 30 Jul 2015, Caspar M. Schwiedrzik wrote: Hi Bruce and Doug, thanks for looking into this and sorry for the delay. The command line we are using is: mri_label2label --srclabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p 8.label --srcsubject y$1 --trglabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp 2.label --trgsubject yx$1 --regmethod surface --hemi lh We have several anatomies from the same subject, acquired on different occasions. We defined labels based on results of an fMRI experiment, and tried to use mri_label2label to map them within subjects from one anatomy to another. As a control, we also wanted to map the Hinds V1 from one anatomy to another, but this is where we ran into these holes. We will make an example subject available for debugging later today. Thanks! Caspar 2015-07-24 12:33 GMT-04:00 Douglas Greve gr...@nmr.mgh.harvard.edu javascript:;: what is your command line? What do you mean by one anatomy to another? On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote: -- Forwarded message -- From: Caspar M. Schwiedrzik cschwie...@rockefeller.edu javascript:; Date: Thursday, July 16, 2015 Subject: problem with mri_label2label - large amount of holes To: Freesurfer@nmr.mgh.harvard.edu javascript:; freesurfer@nmr.mgh.harvard.edu javascript:; Hi! We are doing some analyses in which we map custom labels from one anatomy to another, within subjects. As a control, we also tried to map anatomically defined V1s according to the method by Hinds within subject from one anatomy to another. However, as you can see in the attachment, there are very many holes in the labels after using mri_label2label. This does not happen with smaller labels. Why is this happening and is there a solution? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; 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 javascript:; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; 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
[Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces
Hello, Since surface deformation from WM to inflated surface is a gradual process, I assume that interim surfaces can also be saved and visualized, as I have seen in the ppt of Analyzing the Individual Subject http://surfer.nmr.mgh.harvard.edu/pub/docs/fsl2013/fsrecon.ppt tutorial session (slide #32). I am curious to know which command and options can generate that type of gradual deformations from pial surface to spherical surface, so that viewer can visually track region or points of interest? Best, Saeed ___ 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] qdec problem
The error message is: ERROR: The stats file /Users/i_geschwind/Desktop/qdec_test/CDPAD02WJD_recon/stats/aseg.stats is not found or is too small to be a valid statsfile Have you checked this stat file? It is a text file, so you can just look inside it. On 08/04/2015 10:19 PM, geschwind2013 wrote: Dear suffers Now, I’m running the group analysis using qdec as a beginner. 2 groups, 4patients per each group.. after successful data table loading, I choosed '*Generate Stats Data Tables button’ * * * I found the error message like below,, could you help me ? thanks Hyon-Ah Data table loading completed successfully. SUBJECTS_DIR is '/Users/i_geschwind/Desktop/qdec_test' mkdir -p /Users/i_geschwind/Desktop/qdec_test/qdec/stats_tables/ -- asegstats2table --common-segs --meas volume --tablefile /Users/i_geschwind/Desktop/qdec_test/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects CDPAD02WJD_recon CDPAD09HOH_recon CDPAD26LJC_recon CDPAD28_KEJ2419486 CDPcon02_recon CDPcon03_recon CDPcon04_recon CDPcon05_recon SUBJECTS_DIR : /Users/i_geschwind/Desktop/qdec_test Parsing the .stats files ERROR: The stats file /Users/i_geschwind/Desktop/qdec_test/CDPAD02WJD_recon/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files ERROR: In /usr/pubsw/packages/KWWidgets/CVS-7Aug2010/src/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x6108820): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /Users/i_geschwind/Desktop/qdec_test/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects CDPAD02WJD_recon CDPAD09HOH_recon CDPAD26LJC_recon CDPAD28_KEJ2419486 CDPcon02_recon CDPcon03_recon CDPcon04_recon CDPcon05_recon Stack trace: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /Users/i_geschwind/Desktop/qdec_test/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects CDPAD02WJD_recon CDPAD09HOH_recon CDPAD26LJC_recon CDPAD28_KEJ2419486 CDPcon02_recon CDPcon03_recon CDPcon04_recon CDPcon05_recon while executing vtkTemp2 GenerateStatsDataTables ___ 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.
Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces
Hi Saeed if you specify -w n to mris_inflate or mris_sphere it will save snapshots of the process every nth iteration cheers Bruce On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Since surface deformation from WM to inflated surface is a gradual process, I assume that interim surfaces can also be saved and visualized, as I have seen in the ppt of Analyzing the Individual Subject tutorial session (slide #32). I am curious to know which command and options can generate that type of gradual deformations from pial surface to spherical surface, so that viewer can visually track region or points of interest? Best, Saeed ___ 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] Fwd: Inflated and Spherical Morphing --- Step by step surfaces
Thanks Bruce, and Is there an easy way to make a movie of this deformation? On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Saeed if you specify -w n to mris_inflate or mris_sphere it will save snapshots of the process every nth iteration cheers Bruce On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Since surface deformation from WM to inflated surface is a gradual process, I assume that interim surfaces can also be saved and visualized, as I have seen in the ppt of Analyzing the Individual Subject tutorial session (slide #32). I am curious to know which command and options can generate that type of gradual deformations from pial surface to spherical surface, so that viewer can visually track region or points of interest? Best, Saeed ___ 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.
Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces
you can use convert to take the multiple tiff files that are written and output a dynamic gifti On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Thanks Bruce, and Is there an easy way to make a movie of this deformation? On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Saeed if you specify -w n to mris_inflate or mris_sphere it will save snapshots of the process every nth iteration cheers Bruce On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Since surface deformation from WM to inflated surface is a gradual process, I assume that interim surfaces can also be saved and visualized, as I have seen in the ppt of Analyzing the Individual Subject tutorial session (slide #32). I am curious to know which command and options can generate that type of gradual deformations from pial surface to spherical surface, so that viewer can visually track region or points of interest? Best, Saeed ___ 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] Exception caught for createMorph
Hi, I'm trying to apply a transform that was generated between a native subject's T1 and the cvs_avg35_inMNI152 brain. Per the instructions on the mri_cvs_register page, I ran the transformation, but did not save the .fullCVSmorph.t3md file, so I'd like to regenerate it. Here's my command for doing so: createMorph --out fullCVSmorph.tm3d --template /data/cvs_avg35_inMNI152/mri/brain.mgz --subject /data/orig_subj/mri/brain.mgz --in gcam /data/orig_subj/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z morph el_reg_tocvs_avg35_inMNI152.tm3d which produces the following output: atlas geometry = 256 , 256 , 256 image geometry = 256 , 256 , 256 vox 2 ras atlas = -1.000 0.000 0.000 127.000; 0.000 0.000 1.000 -145.000; 0.000 -1.000 0.000 147.000; 0.000 0.000 0.000 1.000; ras 2 vox image = -1.000 0.000 0.000 127.000; -0.000 -0.000 -1.000 147.000; -0.000 1.000 -0.000 145.000; 0.000 0.000 0.000 1.000; product = 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; transform at origin 0.000; 0.000; 0.000; 1.000; invalid voxel count = 11890277 extension = tm3d Exception caught while loading morph in file el_reg_tocvs_avg35_inMNI152.tm3d This code runs fine for other subjects, so I'm not sure what's wrong here. Does anyone have any suggestions? Thanks, Matt Matthew K. Leonard, PhD Postdoctoral Fellow Department of Neurological Surgery University of California, San Francisco http://changlab.ucsf.edu/ ___ 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] surface reconstruction and quality control
Hi Emma, I'd exclude it and similar images. Or if you have a motion estimate of those subjects (e.g. via adjacent fMRI or diffusion scans), you could use motion as a covariate in your statistics. Motion does bias measurements (smaller cortical GM volume), see e.g. here: http://dx.doi.org/10.1016/j.neuroimage.2014.12.006 http://reuter.mit.edu/papers/reuter-motion14.pdf Best, Martin On 08/05/2015 02:55 PM, Emma Thompson wrote: Hi Freesurfers, I have a question regarding quality control. One of my subjects has pretty moderate ringing in their mprage image (presumably due to motion), I was thinking I should be excluding this subject, however I ran the subject through the pipeline anyway and I see that the segmentation and surfaces look ok. I'm wondering if based on this I should go ahead and include this subject for my analyses. I have attached a screenshot of the mprage and was hoping someone would take a look and give me their expert opinion. Thanks for you help! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu ___ 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] mri_convert IMA to MGZ
Hi freesurfers, I want to localize electrode locations from a NHP CT scan, am i able to do that with tkmedit without coregistering first? I don't need all the parcellations of a specific atlas, just the RAS coordinates. Also, the CT images are IMA files. Is there a way to convert from IMA to MGZ, something like: mri_convert -i first_ct_dicom.dcm -o ct.mgz I tried this and it created a file but i want to make sure i didn't need to make any specifications in the command. Thanks, m ___ 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] ID-swapping freesurfer data?
Thanks! One complication I'm seeing is that when I uncompress, say, an .mgz file, the old subject number is still embedded in some text near the end of the file*. Since we want to change these ID numbers for de-identification purposes, we'd need to change them there, too. Is there a way to either strip those things or edit them? Thanks! -Nate * For example: P/studies/STUDY/DATA/mri/processed/freesurfer/IDENTIFIER/mri/transforms/talairach.xfm UNKNOWN @AutoAlign 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mri_convert /studies/STUDY/DATA/mri/processed/IDENTIFIER/anat/T1High_native1.nii /studies/STUDY/DATA/mri/processed/freesurfer/IDENTIFIER/mri/orig/001.mgz ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/25-21:51:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: USER Machine: MACHINE Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 mri_convert /studies/STUDY/DATA/mri/processed/freesurfer/IDENTIFIER/mri/rawavg.mgz /studies/STUDY/DATA/mri/processed/freesurfer/IDENTIFIER/mri/orig.mgz --conform ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/25-21:54:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: USER Machine: MACHINE Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 On Mon, Aug 3, 2015 at 12:03 PM Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I think that should work without problem. On 08/03/2015 12:51 PM, Nate Vack wrote: Hi all, We're looking to change the ID system we're using for some freesurfer data. Will doing do be as simple as renaming our single-subject data directories and restarting analysis from that point, or would we need to do something more complicated? Many thanks, -Nate ___ 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 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] Fwd: Inflated and Spherical Morphing --- Step by step surfaces
I am a bit confused, mri_convert is basically used to convert 3D models (e.g. .inflate file types) to tiff images? Will it be captured from a specified perspective and 1 tiff for each volume? And these tiff files will be combined to generate animated gif? What is dynamic gifti? On Wed, Aug 5, 2015 at 3:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: you can use convert to take the multiple tiff files that are written and output a dynamic gifti On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Thanks Bruce, and Is there an easy way to make a movie of this deformation? On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Saeed if you specify -w n to mris_inflate or mris_sphere it will save snapshots of the process every nth iteration cheers Bruce On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Since surface deformation from WM to inflated surface is a gradual process, I assume that interim surfaces can also be saved and visualized, as I have seen in the ppt of Analyzing the Individual Subject tutorial session (slide #32). I am curious to know which command and options can generate that type of gradual deformations from pial surface to spherical surface, so that viewer can visually track region or points of interest? Best, Saeed ___ 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] surface reconstruction and quality control
Thanks Martin, I will exclude this subject from my analyses. On Wed, Aug 5, 2015 at 4:18 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Emma, I'd exclude it and similar images. Or if you have a motion estimate of those subjects (e.g. via adjacent fMRI or diffusion scans), you could use motion as a covariate in your statistics. Motion does bias measurements (smaller cortical GM volume), see e.g. here: http://dx.doi.org/10.1016/j.neuroimage.2014.12.006 http://reuter.mit.edu/papers/reuter-motion14.pdf Best, Martin On 08/05/2015 02:55 PM, Emma Thompson wrote: Hi Freesurfers, I have a question regarding quality control. One of my subjects has pretty moderate ringing in their mprage image (presumably due to motion), I was thinking I should be excluding this subject, however I ran the subject through the pipeline anyway and I see that the segmentation and surfaces look ok. I'm wondering if based on this I should go ahead and include this subject for my analyses. I have attached a screenshot of the mprage and was hoping someone would take a look and give me their expert opinion. Thanks for you help! ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu ___ 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.
Re: [Freesurfer] surface reconstruction and quality control
Hi Emma, Martin, I'd like to offer a different perspective. Based on what you showed, I thought that the motion related ringing wasn't too bad, and I'd expect that FS would handle that data quite well, which is what you indicated was indeed the case. If we all started excluding data of the sort that you showed, then there are going to be a lot of studies that would have to exclude a chunk of subjects. If that is the worst motion related artifact in your study, then you've been very successful at collecting good quality structurals! cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Emma Thompson vonecono...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, August 5, 2015 4:34 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface reconstruction and quality control Thanks Martin, I will exclude this subject from my analyses. On Wed, Aug 5, 2015 at 4:18 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Emma, I'd exclude it and similar images. Or if you have a motion estimate of those subjects (e.g. via adjacent fMRI or diffusion scans), you could use motion as a covariate in your statistics. Motion does bias measurements (smaller cortical GM volume), see e.g. here: http://dx.doi.org/10.1016/j.neuroimage.2014.12.006 http://reuter.mit.edu/papers/reuter-motion14.pdf Best, Martin On 08/05/2015 02:55 PM, Emma Thompson wrote: Hi Freesurfers, I have a question regarding quality control. One of my subjects has pretty moderate ringing in their mprage image (presumably due to motion), I was thinking I should be excluding this subject, however I ran the subject through the pipeline anyway and I see that the segmentation and surfaces look ok. I'm wondering if based on this I should go ahead and include this subject for my analyses. I have attached a screenshot of the mprage and was hoping someone would take a look and give me their expert opinion. Thanks for you help! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: 1-617-724-5652 Web : http://reuter.mit.edu ___ 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. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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.
Re: [Freesurfer] ID-swapping freesurfer data?
the easiest thing to do is to read them into matlab and write them back out. I think that strips all the tags (which is where the subject name is stored) On Wed, 5 Aug 2015, Nate Vack wrote: Thanks! One complication I'm seeing is that when I uncompress, say, an .mgz file, the old subject number is still embedded in some text near the end of the file*. Since we want to change these ID numbers for de-identification purposes, we'd need to change them there, too. Is there a way to either strip those things or edit them? Thanks! -Nate * For example: P/studies/STUDY/DATA/mri/processed/freesurfer/IDENTIFIER/mri/transforms/tal airach.xfm UNKNOWN @AutoAlign 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mri_convert /studies/STUDY/DATA/mri/processed/IDENTIFIER/anat/T1High_native1.nii /studies/STUDY/DATA/mri/processed/freesurfer/IDENTIFIER/mri/orig/001.mgz ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/25-21:51:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: USER Machine: MACHINE Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 mri_convert /studies/STUDY/DATA/mri/processed/freesurfer/IDENTIFIER/mri/rawavg.mgz /studies/STUDY/DATA/mri/processed/freesurfer/IDENTIFIER/mri/orig.mgz --conform ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/25-21:54:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: USER Machine: MACHINE Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 On Mon, Aug 3, 2015 at 12:03 PM Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I think that should work without problem. On 08/03/2015 12:51 PM, Nate Vack wrote: Hi all, We're looking to change the ID system we're using for some freesurfer data. Will doing do be as simple as renaming our single-subject data directories and restarting analysis from that point, or would we need to do something more complicated? Many thanks, -Nate ___ 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 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] Fwd: Inflated and Spherical Morphing --- Step by step surfaces
not mri_convert, convert. And sorry, I mean a dynamic gif: man convert NAME convert - convert between image formats as well as resize an image, blur, crop, despeckle, dither, draw on, flip, join, re-sample, and much more. SYNOPSIS convert [input-options] input-file [output-options] output-file OVERVIEW The convert program is a member of the ImageMagick(1) suite of tools. Use it to convert between image formats as well as resize an image, blur, crop, despeckle, dither, draw on, flip, join, re-sample, and much more. For more information about the convert command, point your browser to file:///usr/share/doc/ImageMag- cheers Bruce On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: I am a bit confused, mri_convert is basically used to convert 3D models (e.g. .inflate file types) to tiff images? Will it be captured from a specified perspective and 1 tiff for each volume?And these tiff files will be combined to generate animated gif? What is dynamic gifti? On Wed, Aug 5, 2015 at 3:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: you can use convert to take the multiple tiff files that are written and output a dynamic gifti On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Thanks Bruce, and Is there an easy way to make a movie of this deformation? On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Saeed if you specify -w n to mris_inflate or mris_sphere it will save snapshots of the process every nth iteration cheers Bruce On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Since surface deformation from WM to inflated surface is a gradual process, I assume that interim surfaces can also be saved and visualized, as I have seen in the ppt of Analyzing the Individual Subject tutorial session (slide #32). I am curious to know which command and options can generate that type of gradual deformations from pial surface to spherical surface, so that viewer can visually track region or points of interest? Best, Saeed ___ 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.
[Freesurfer] [possible Bug] Unexpected parse error during reading of lh.area
From: zorze...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Date: Thu, 6 Aug 2015 07:42:40 +0200 Hi, The recon pipeline outputed an apparently correct file, which happen to confuse freesurfer reading functions. I attached a slightly-altered file named lh.data_crash which have the same problem. The other file named lh.data_nocrash seems to be parsed fine, despite differing by only 1 float-value somewhere in the middle of the data section. Original file was lh.area The mri_info command outputs some meaningless values; and the mris_calc command bails out. $ mri_info lh.data_crash WARNING: # of slices=-45 in header - assuming 124... Volume information for lh.data_crash type: unknown dimensions: 3391 x 2677 x 124 voxel sizes: -0., -0., -0. type: SHORT (4) fov: 0.246 dof: 0 xstart: 548.5, xend: 5149214485235471024091229374082187264.0 ystart: -0.0, yend: -0.0 zstart: -1008284058362807724504196555655348224.0, zend: 0.0 ... $ mri_info lh.data_nocrash Volume information for lh.data_nocrash type: curv dimensions: 124254 x 1 x 1 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 124254.000 dof: 0 xstart: -62127.0, xend: 62127.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.0 ... The difference between the two files are a single value change (4 bytes) at offset 1095 (15+4*1095'th byte), although other alteration are possible which avoid the crash too. This happens on Freesurfer version 5.3.0, and also 5.1.0, and 6-beta, on all arch i could test, which are RedHat 6.6 (64bits), Ubuntu 10.x (32bits), and MacOSX 10.8 (64bits) Note: to preserve privacy, the original map values have been replaced by a dummy 42.0 for most of the file, since i believe actual data is irrelevant here. I couldn't track the problem further, as i only have (stripped) binaries here. ___ 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] registering NHP data
There are 2 papers the describe the atlas and method for normalization. (1) McLaren et al. 2009. NeuroImage. A population-average MRI-based atlas collection of the rhesus macaque. (2) McLaren et al. 2010. Methods. Rhesus macaque brain morphometry: A methodological comparison of voxel-wise approaches. If you create a second image with a sphere at the electrode location, then you can normalize the MRI and apply the parameters to the image of electrode location spheres, then you can look up in the book which region the electrode was located. Best Regards, Donald McLaren, PhD On Wed, Aug 5, 2015 at 9:45 AM, Borzello, Mia mborze...@partners.org wrote: Awesome that you guys are working a parcellation! In the meantime, if I wanted to try to use the atlases you suggested, how would I go about processing the data? Is there documentation I can follow? Thanks so much, Mia -- *From:* MCLAREN, Donald [mclaren.don...@gmail.com] *Sent:* Tuesday, August 04, 2015 9:36 AM *To:* Borzello, Mia *Subject:* Re: [Freesurfer] registering NHP data Mia, You could use the 112RM-SL atlas for normalization and then use the Saleem-Logothetis Atlas for localization. Hopefully, by August, we'll have a parcellation on the the MR image so that localization can be done automatically. Best Regards, Donald McLaren, PhD On Mon, Aug 3, 2015 at 2:01 PM, Borzello, Mia mborze...@partners.org wrote: Hi Freesurfer experts, Does Freesurfer have a separate pipeline for registering NHP data? I am trying to register macaque data and localize the implanted electrodes, but the normal protocol errored. I did a google search and found this- is this what I should be using?: https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData I downloaded the scripts but I'm not sure what commands I'm supposed to be running, etc. Any guidance you can give would be must appreciated! Thanks, m ___ 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 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] Head Motion -- was: surface reconstruction and quality control
I forgot to mention, we used the QC protocol described here: http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information-investigators/qc with a manual of examples: http://cbs.fas.harvard.edu/usr/mcmains/CBS_MRI_Qualitative_Quality_Control_Manual.pdf where Fig. 6 in our paper shows the results when removing the 'fail' cases, so fail is basically everything 7mm/sec and some cases below that. The warn category is more heterogeneous and has a range of low and medium motion cases. Best, Martin On 08/05/2015 08:25 PM, Martin Reuter wrote: Yes, I wanted to make those images available, but this was not in the consent forms and I don't think it will be possible to re-consent the subjects. I pushed that a little a while ago, will try again. Martin On 08/05/2015 08:17 PM, Harms, Michael wrote: Hi Martin, I totally agree that we need robust approaches to either correct for motion during the structurals in real time (as you guys have been working on with your vNav sequence), or start at least quantifying motion during structural imaging (e.g,. again by using the same vNav sequence, but just using it to estimate the motion). It seems challenging to me though, and potentially somewhat arbitrary (i.e., variable across investigators), to start making decisions to exclude scans with moderate to mild movement related ringing, which is such a common problem. At least not without a better understanding of how a given degree of ringing translates to your quantitative X mm/min of motion measurement. Along those lines, do you guys have any illustrations of what X mm/min of motion looks like in the actual structurals for varying values of X? It would be really helpful for contextualizing your paper if a set of images were available showing that mapping. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu From: Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu Reply-To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, August 5, 2015 6:55 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Head Motion -- was: surface reconstruction and quality control Hi Michael, we showed that motion (even the one that you cannot really see in the image) produces biased measurements (and not just in FreeSurfer but also other methods). FS handels all kinds of data, even really crappy images, and that is exactly the problem, as these measurements can be severely biased and most users don't even check their images. We found that 1mm/min of motion reduces gray matter volume by 0.7%. This is a lot, given that the best still scans in our healthy young adult test subjects were at 2-3mm/min (that was the no-motion scan). QC was able to remove scans with above 6 or 7mm/min. So on average even after QC and removal of scans with motion problems, you end up having lots of cases with 5 to 7mm/min motion = 3.5% to 5% reduced GM volume. I think, (maybe someone here knows better), that is the atrophy of a healthy control in 5 years and probably more than the yearly loss in an advanced AD or HD patient. Depending on the study, it may very well be possible that the disease group moves more than the control group, the older group more than the younger (unless you have kids, who move a lot) and also longitudinally that motion increases over time. This will bias your study. You are right, that removing single (worst case) images will not cut it. The problem is far worse. We need a way to either -correct motion online -at least quantify motion during structural imaging to use as a covariate or for filtering severe cases. That is why I recommended to use fMRI or diffusion close to the structural to estimate the motion there. That should give you an idea (of course does not replace manual QC for filtering bad cases). We need to avoid running drug studies that basically quantify the amount of reduced motion with an expensive MRI scan. Anyway, I would say, if in doubt remove it. To at least limit the influence of motion bias to the 3-5% range (which is still too large). Cheers, Martin On 08/05/2015 05:44 PM, Harms, Michael wrote: Hi Emma, Martin, I'd like to offer a different perspective. Based on what you showed, I thought that the motion related ringing wasn't too bad, and I'd expect that FS would handle that data quite well, which is what you indicated was indeed the case. If we all started excluding data of the sort that you showed, then there are going to be a lot
[Freesurfer] (no subject)
Hi, The recon pipeline outputed an apparently correct file, which happen to confuse freesurfer reading functions. I attached a slightly-altered file named lh.data_crash which have the same problem. The other file named lh.data_nocrash seems to be parsed fine, despite differing by only 1 float-value somewhere in the middle of the data section. Original file was lh.area The mri_info command outputs some meaningless values; and the mris_calc command bails out. $ mri_info lh.data_crash WARNING: # of slices=-45 in header - assuming 124... Volume information for lh.data_crash type: unknown dimensions: 3391 x 2677 x 124 voxel sizes: -0., -0., -0. type: SHORT (4) fov: 0.246 dof: 0 xstart: 548.5, xend: 5149214485235471024091229374082187264.0 ystart: -0.0, yend: -0.0 zstart: -1008284058362807724504196555655348224.0, zend: 0.0 ... $ mri_info lh.data_nocrash Volume information for lh.data_nocrash type: curv dimensions: 124254 x 1 x 1 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 124254.000 dof: 0 xstart: -62127.0, xend: 62127.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.0 ... The difference between the two files are a single value change (4 bytes) at offset 1095 (15+4*1095'th byte), although other alteration are possible which avoid the crash too. This happens on Freesurfer version 5.3.0, and also 5.1.0, and 6-beta, on all arch i could test, which are RedHat 6.6 (64bits), Ubuntu 10.x (32bits), and MacOSX 10.8 (64bits) Note: to preserve privacy, the original map values have been replaced by a dummy 42.0 for most of the file, since i believe actual data is irrelevant here. I couldn't track the problem further, as i only have (stripped) binaries here. lh.data_nocrash.gz Description: GNU Zip compressed data lh.data_crash.gz Description: GNU Zip compressed data ___ 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] Head Motion -- was: surface reconstruction and quality control
Hi Michael, we showed that motion (even the one that you cannot really see in the image) produces biased measurements (and not just in FreeSurfer but also other methods). FS handels all kinds of data, even really crappy images, and that is exactly the problem, as these measurements can be severely biased and most users don't even check their images. We found that 1mm/min of motion reduces gray matter volume by 0.7%. This is a lot, given that the best still scans in our healthy young adult test subjects were at 2-3mm/min (that was the no-motion scan). QC was able to remove scans with above 6 or 7mm/min. So on average even after QC and removal of scans with motion problems, you end up having lots of cases with 5 to 7mm/min motion = 3.5% to 5% reduced GM volume. I think, (maybe someone here knows better), that is the atrophy of a healthy control in 5 years and probably more than the yearly loss in an advanced AD or HD patient. Depending on the study, it may very well be possible that the disease group moves more than the control group, the older group more than the younger (unless you have kids, who move a lot) and also longitudinally that motion increases over time. This will bias your study. You are right, that removing single (worst case) images will not cut it. The problem is far worse. We need a way to either -correct motion online -at least quantify motion during structural imaging to use as a covariate or for filtering severe cases. That is why I recommended to use fMRI or diffusion close to the structural to estimate the motion there. That should give you an idea (of course does not replace manual QC for filtering bad cases). We need to avoid running drug studies that basically quantify the amount of reduced motion with an expensive MRI scan. Anyway, I would say, if in doubt remove it. To at least limit the influence of motion bias to the 3-5% range (which is still too large). Cheers, Martin On 08/05/2015 05:44 PM, Harms, Michael wrote: Hi Emma, Martin, I'd like to offer a different perspective. Based on what you showed, I thought that the motion related ringing wasn't too bad, and I'd expect that FS would handle that data quite well, which is what you indicated was indeed the case. If we all started excluding data of the sort that you showed, then there are going to be a lot of studies that would have to exclude a chunk of subjects. If that is the worst motion related artifact in your study, then you've been very successful at collecting good quality structurals! cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu From: Emma Thompson vonecono...@gmail.com mailto:vonecono...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, August 5, 2015 4:34 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface reconstruction and quality control Thanks Martin, I will exclude this subject from my analyses. On Wed, Aug 5, 2015 at 4:18 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu wrote: Hi Emma, I'd exclude it and similar images. Or if you have a motion estimate of those subjects (e.g. via adjacent fMRI or diffusion scans), you could use motion as a covariate in your statistics. Motion does bias measurements (smaller cortical GM volume), see e.g. here: http://dx.doi.org/10.1016/j.neuroimage.2014.12.006 http://reuter.mit.edu/papers/reuter-motion14.pdf Best, Martin On 08/05/2015 02:55 PM, Emma Thompson wrote: Hi Freesurfers, I have a question regarding quality control. One of my subjects has pretty moderate ringing in their mprage image (presumably due to motion), I was thinking I should be excluding this subject, however I ran the subject through the pipeline anyway and I see that the segmentation and surfaces look ok. I'm wondering if based on this I should go ahead and include this subject for my analyses. I have attached a screenshot of the mprage and was hoping someone would take a look and give me their expert opinion. Thanks for you help! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT
Re: [Freesurfer] Head Motion -- was: surface reconstruction and quality control
Hi Martin, I totally agree that we need robust approaches to either correct for motion during the structurals in real time (as you guys have been working on with your vNav sequence), or start at least quantifying motion during structural imaging (e.g,. again by using the same vNav sequence, but just using it to estimate the motion). It seems challenging to me though, and potentially somewhat arbitrary (i.e., variable across investigators), to start making decisions to exclude scans with moderate to mild movement related ringing, which is such a common problem. At least not without a better understanding of how a given degree of ringing translates to your quantitative X mm/min of motion measurement. Along those lines, do you guys have any illustrations of what X mm/min of motion looks like in the actual structurals for varying values of X? It would be really helpful for contextualizing your paper if a set of images were available showing that mapping. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Martin Reuter mreu...@nmr.mgh.harvard.edu Reply-To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Date: Wednesday, August 5, 2015 6:55 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Head Motion -- was: surface reconstruction and quality control Hi Michael, we showed that motion (even the one that you cannot really see in the image) produces biased measurements (and not just in FreeSurfer but also other methods). FS handels all kinds of data, even really crappy images, and that is exactly the problem, as these measurements can be severely biased and most users don't even check their images. We found that 1mm/min of motion reduces gray matter volume by 0.7%. This is a lot, given that the best still scans in our healthy young adult test subjects were at 2-3mm/min (that was the no-motion scan). QC was able to remove scans with above 6 or 7mm/min. So on average even after QC and removal of scans with motion problems, you end up having lots of cases with 5 to 7mm/min motion = 3.5% to 5% reduced GM volume. I think, (maybe someone here knows better), that is the atrophy of a healthy control in 5 years and probably more than the yearly loss in an advanced AD or HD patient. Depending on the study, it may very well be possible that the disease group moves more than the control group, the older group more than the younger (unless you have kids, who move a lot) and also longitudinally that motion increases over time. This will bias your study. You are right, that removing single (worst case) images will not cut it. The problem is far worse. We need a way to either -correct motion online -at least quantify motion during structural imaging to use as a covariate or for filtering severe cases. That is why I recommended to use fMRI or diffusion close to the structural to estimate the motion there. That should give you an idea (of course does not replace manual QC for filtering bad cases). We need to avoid running drug studies that basically quantify the amount of reduced motion with an expensive MRI scan. Anyway, I would say, if in doubt remove it. To at least limit the influence of motion bias to the 3-5% range (which is still too large). Cheers, Martin On 08/05/2015 05:44 PM, Harms, Michael wrote: Hi Emma, Martin, I'd like to offer a different perspective. Based on what you showed, I thought that the motion related ringing wasn't too bad, and I'd expect that FS would handle that data quite well, which is what you indicated was indeed the case. If we all started excluding data of the sort that you showed, then there are going to be a lot of studies that would have to exclude a chunk of subjects. If that is the worst motion related artifact in your study, then you've been very successful at collecting good quality structurals! cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Emma Thompson vonecono...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, August 5, 2015 4:34 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface reconstruction and quality control Thanks Martin, I will exclude this subject from my analyses. On Wed, Aug 5, 2015 at 4:18 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Emma, I'd exclude it and similar images. Or if you have a motion estimate of those
Re: [Freesurfer] Head Motion -- was: surface reconstruction and quality control
Yes, I wanted to make those images available, but this was not in the consent forms and I don't think it will be possible to re-consent the subjects. I pushed that a little a while ago, will try again. Martin On 08/05/2015 08:17 PM, Harms, Michael wrote: Hi Martin, I totally agree that we need robust approaches to either correct for motion during the structurals in real time (as you guys have been working on with your vNav sequence), or start at least quantifying motion during structural imaging (e.g,. again by using the same vNav sequence, but just using it to estimate the motion). It seems challenging to me though, and potentially somewhat arbitrary (i.e., variable across investigators), to start making decisions to exclude scans with moderate to mild movement related ringing, which is such a common problem. At least not without a better understanding of how a given degree of ringing translates to your quantitative X mm/min of motion measurement. Along those lines, do you guys have any illustrations of what X mm/min of motion looks like in the actual structurals for varying values of X? It would be really helpful for contextualizing your paper if a set of images were available showing that mapping. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu From: Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu Reply-To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, August 5, 2015 6:55 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Head Motion -- was: surface reconstruction and quality control Hi Michael, we showed that motion (even the one that you cannot really see in the image) produces biased measurements (and not just in FreeSurfer but also other methods). FS handels all kinds of data, even really crappy images, and that is exactly the problem, as these measurements can be severely biased and most users don't even check their images. We found that 1mm/min of motion reduces gray matter volume by 0.7%. This is a lot, given that the best still scans in our healthy young adult test subjects were at 2-3mm/min (that was the no-motion scan). QC was able to remove scans with above 6 or 7mm/min. So on average even after QC and removal of scans with motion problems, you end up having lots of cases with 5 to 7mm/min motion = 3.5% to 5% reduced GM volume. I think, (maybe someone here knows better), that is the atrophy of a healthy control in 5 years and probably more than the yearly loss in an advanced AD or HD patient. Depending on the study, it may very well be possible that the disease group moves more than the control group, the older group more than the younger (unless you have kids, who move a lot) and also longitudinally that motion increases over time. This will bias your study. You are right, that removing single (worst case) images will not cut it. The problem is far worse. We need a way to either -correct motion online -at least quantify motion during structural imaging to use as a covariate or for filtering severe cases. That is why I recommended to use fMRI or diffusion close to the structural to estimate the motion there. That should give you an idea (of course does not replace manual QC for filtering bad cases). We need to avoid running drug studies that basically quantify the amount of reduced motion with an expensive MRI scan. Anyway, I would say, if in doubt remove it. To at least limit the influence of motion bias to the 3-5% range (which is still too large). Cheers, Martin On 08/05/2015 05:44 PM, Harms, Michael wrote: Hi Emma, Martin, I'd like to offer a different perspective. Based on what you showed, I thought that the motion related ringing wasn't too bad, and I'd expect that FS would handle that data quite well, which is what you indicated was indeed the case. If we all started excluding data of the sort that you showed, then there are going to be a lot of studies that would have to exclude a chunk of subjects. If that is the worst motion related artifact in your study, then you've been very successful at collecting good quality structurals! cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu From: Emma Thompson vonecono...@gmail.com
