Re: [Freesurfer] prefrontal cortex label
hi the full error message is reading input surface /XX/surf/lh.pial... reading input pial surface /XX/surf/lh.pial... reading input white surface //X/surf/lh.white... mris_anatomical_stats: could not parse 1697283th line '60529 -5.365 -17' in label file subj: could not read label file (null) On Mon, Nov 24, 2014 at 4:56 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: What is the full terminal output and error msg? On 11/21/2014 04:14 AM, Anna Jonsson wrote: hi, I have tried to make prefrotnal cortex label by doing first mri_annotation2label --subject $subject --hemi rh --outdir $subject/label mri_mergelabels -i lh.caudalanteriorcingulate.label -i lh.caudalmiddlefrontal.label -i lh.lateralorbitofrontal.label -i lh.medialorbitofrontal.label -i lh.parsopercularis.label -i lh.parsorbitalis.label -i lh.parstriangularis.label -i lh.rostralanteriorcingulate.label -i lh.rostralmiddlefrontal.label -i lh.superiorfrontal.label -i lh.lateralorbitofrontal.label -o lh.prefrontalcortex.label -d /directory/subject/label which does create a label called x.prefrontalcortex.label in each persons directory. then however when i try to do mris_anatomical_stats -l $SUBJECTS_DIR/$subject/label/lh.prefrontalcortex.label $subject lh pial | grep thickness left_prefrontal i get error and say it cant find label. any pointers on what im doing wrong? thank you ___ 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.
[Freesurfer] prefrontal cortex label
hi, I have tried to make prefrotnal cortex label by doing first mri_annotation2label --subject $subject --hemi rh --outdir $subject/label mri_mergelabels -i lh.caudalanteriorcingulate.label -i lh.caudalmiddlefrontal.label -i lh.lateralorbitofrontal.label -i lh.medialorbitofrontal.label -i lh.parsopercularis.label -i lh.parsorbitalis.label -i lh.parstriangularis.label -i lh.rostralanteriorcingulate.label -i lh.rostralmiddlefrontal.label -i lh.superiorfrontal.label -i lh.lateralorbitofrontal.label -o lh.prefrontalcortex.label -d /directory/subject/label which does create a label called x.prefrontalcortex.label in each persons directory. then however when i try to do mris_anatomical_stats -l $SUBJECTS_DIR/$subject/label/lh.prefrontalcortex.label $subject lh pial | grep thickness left_prefrontal i get error and say it cant find label. any pointers on what im doing wrong? thank you ___ 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] prefrontal cortex label
hi, anyone can help with this? On Tue, Nov 4, 2014 at 4:43 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I don't know. Maybe someone else can weigh in. doug On 11/04/2014 07:38 AM, Anna Jonsson wrote: thank you. which labels are normally included as prefrontal cortex for freesurfer purposes? On Thu, Oct 23, 2014 at 5:04 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: You can use mri_annotation2label to break up the annotation into individual labels, then use mris_label2annot to recombine selected labels into an annotation or use mri_merge_label to merge them into a single label. All you have to do is decide with labels define prefontal doug On 10/23/2014 10:25 AM, Anna Jonsson wrote: Dear group, Is there a way to create a prefrontal cortex label in fresurfer? if so, please tell me the exact steps to do so, I am very confused. Thank you, Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto: 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 -- 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 ___ 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] prefrontal cortex label
thank you. which labels are normally included as prefrontal cortex for freesurfer purposes? On Thu, Oct 23, 2014 at 5:04 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You can use mri_annotation2label to break up the annotation into individual labels, then use mris_label2annot to recombine selected labels into an annotation or use mri_merge_label to merge them into a single label. All you have to do is decide with labels define prefontal doug On 10/23/2014 10:25 AM, Anna Jonsson wrote: Dear group, Is there a way to create a prefrontal cortex label in fresurfer? if so, please tell me the exact steps to do so, I am very confused. Thank you, Anna ___ 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.
[Freesurfer] prefrontal cortex label
Dear group, Is there a way to create a prefrontal cortex label in fresurfer? if so, please tell me the exact steps to do so, I am very confused. Thank you, Anna ___ 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] lgi for longitudinal scans
hi Martin, I just tried this and it resulted in errors/ Do I not have to specify a flag for the baseid or for each subject, eg -s? What I did (according to your suggestion) recon-all -long XXX_1.long XXX_2.long -localGI This did not work? Do you know why potentially? On Wed, Mar 26, 2014 at 3:28 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Anna, no, you would still do: recon-all -long tpid baseid -localGI just not use the '-all'. Best, Martin On 03/26/2014 11:12 AM, Anna Jonsson wrote: thank you. But if the lnog process has already been done and these induviduals already have long directories so to speak, I would just put the lgi flag on as normal but just replace the subject name with the long subject name eg ? recon-all -s _long -localGI Thank you On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Anna, for the image processing, you just add the lgi flag to the regular longitudinal recon-all command recon-all -long …… -lgi for the analysis after that you use the long directories. Best, Martin On Mar 15, 2014, at 10:04 AM, Anna Jonsson ajonsso...@gmail.com wrote: Dear group, If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the normal baseline command on the .long data? thank you, kind wishes Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu 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. -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu 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.
Re: [Freesurfer] qdec error
hi, i never recieved answer for this problem...any ideas? On Tue, Jul 8, 2014 at 11:13 AM, Anna Jonsson ajonsso...@gmail.com wrote: Dear group, I now have error loading my qdec table into qdec, for this error fsid column:1 Number of factors: 8 Number of subjects: 168 ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: age_demeaned for subject XXX However those 5 of those factors are continious, and Im assuming the problem is that for some reason qdec thinks they are categorical, and should have a file with levels corresponding to them. How I make freesurfer know they are continuous? Kind Wishes, Linn ___ 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] qdec error
Dear group, I now have error loading my qdec table into qdec, for this error fsid column:1 Number of factors: 8 Number of subjects: 168 ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: age_demeaned for subject XXX However those 5 of those factors are continious, and Im assuming the problem is that for some reason qdec thinks they are categorical, and should have a file with levels corresponding to them. How I make freesurfer know they are continuous? Kind Wishes, Linn ___ 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] visualize group analysis results of qdec
I also have this problem now. did this query ever resolve? On Wed, Jun 4, 2014 at 10:55 PM, Qijing Yu yu.qijing@gmail.com wrote: Hello FreeSufers, I ran several analyses in qdec, and now have problem visualize previous analyses results...which sounds dumb... Please let me know if you have any ideas. I used fsaverage. I found this page http://freesurfer.net/fswiki/FsTutorial/Visualization using tksurfer, but it needs to do the make_average. And it mentioned some pre-computed results, I thought which would be the results of analyses via command line. Does this apply to the results by qdec? I also found the following command using Freeview: freeview -f SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d But I don't know which part of the command should I change. I tried the command as it is above anyway and the error is: Unrecognized sub-option flag 'annot_outline' Many thanks! All the best, Qijing ___ 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] free-surfer longitudinal Qdec table
thank you. and one other question; rather than putting years as the time variable, can i do time 1 (for baseline) and 2 (for follow-up), and jsut control for time between scans instead? On Fri, Jun 13, 2014 at 5:42 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Anna, whenever it says qdec-long the table is in qdec format (with a fsid-base as second column. It would then use the longitudinally processed results, which is what you want , both for lme and 2 stage model. Best Martin Sent via my smartphone, please excuse brevity. Original message From: Anna Jonsson Date:06/09/2014 3:47 PM (GMT+01:00) To: Freesurfer support list Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table Hi, sorry for more questions, but i have a few. When running the first step of the lme implemented tools, doing the command *mris_preproc* --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh (assembles your thickness data into a single lh.thickness.mgh file), am I correct that this just needs to be a normal cross-sectional qdec table that free surfer subsequently makes into long format by --qdec-long option? so the lnogitudinal qdec table is only used in the two stage modell? This too just uses the cross-sectionally derived scans? Im confused where the .long runs become used? thank you and kind wishes On Wed, Jun 4, 2014 at 5:01 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Anna, Fsid is the cross sectionall name without the .long. Best martin Sent via my smartphone, please excuse brevity. Original message From: Anna Jonsson Date:06/04/2014 7:22 AM (GMT-05:00) To: Freesurfer support list Subject: [Freesurfer] free-surfer longitudinal Qdec table Hi, I would like to make my freesurfer longitudinal qdec table for the to use in the lme matlab tools. However, does the fsid need to refer to the longitidunally derived subject; eg XXX.long, or the cross-sectionally derived subject, eg XXX. Im not sure based on the specification online. Kind Regards Anna ___ 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] free-surfer longitudinal Qdec table
Thank you. I just another question about the fsid groupings for the qdec table for lme. If in the qdec I specify only the fisid (eg nt the longitudinally processed subject with XX.long), and the XX.longs are in a different folder, than how when I do the matlab lme tools does freesurfer know to use the XXX.long scans? This is confusing me. Thanks for help,. Regards Anna On Tue, Jun 24, 2014 at 11:26 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Anna I am not a statistician, but I would not control for duration separately, but rather use the time variable for that. It does not need to be in years (can be days out months). Measures closer in time are more correlated than measures further apart. Lme makes use of that information through the time variable. Best Martin Best Martin Sent via my smartphone, please excuse brevity. Original message From: Anna Jonsson Date:06/24/2014 11:52 AM (GMT+01:00) To: Martin Reuter Cc: Freesurfer support list Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table thank you. and one other question; rather than putting years as the time variable, can i do time 1 (for baseline) and 2 (for follow-up), and jsut control for time between scans instead? On Fri, Jun 13, 2014 at 5:42 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Anna, whenever it says qdec-long the table is in qdec format (with a fsid-base as second column. It would then use the longitudinally processed results, which is what you want , both for lme and 2 stage model. Best Martin Sent via my smartphone, please excuse brevity. Original message From: Anna Jonsson Date:06/09/2014 3:47 PM (GMT+01:00) To: Freesurfer support list Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table Hi, sorry for more questions, but i have a few. When running the first step of the lme implemented tools, doing the command *mris_preproc* --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh (assembles your thickness data into a single lh.thickness.mgh file), am I correct that this just needs to be a normal cross-sectional qdec table that free surfer subsequently makes into long format by --qdec-long option? so the lnogitudinal qdec table is only used in the two stage modell? This too just uses the cross-sectionally derived scans? Im confused where the .long runs become used? thank you and kind wishes On Wed, Jun 4, 2014 at 5:01 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Anna, Fsid is the cross sectionall name without the .long. Best martin Sent via my smartphone, please excuse brevity. Original message From: Anna Jonsson Date:06/04/2014 7:22 AM (GMT-05:00) To: Freesurfer support list Subject: [Freesurfer] free-surfer longitudinal Qdec table Hi, I would like to make my freesurfer longitudinal qdec table for the to use in the lme matlab tools. However, does the fsid need to refer to the longitidunally derived subject; eg XXX.long, or the cross-sectionally derived subject, eg XXX. Im not sure based on the specification online. Kind Regards Anna ___ 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] free-surfer longitudinal Qdec table
Hi, sorry for more questions, but i have a few. When running the first step of the lme implemented tools, doing the command *mris_preproc* --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh (assembles your thickness data into a single lh.thickness.mgh file), am I correct that this just needs to be a normal cross-sectional qdec table that free surfer subsequently makes into long format by --qdec-long option? so the lnogitudinal qdec table is only used in the two stage modell? This too just uses the cross-sectionally derived scans? Im confused where the .long runs become used? thank you and kind wishes On Wed, Jun 4, 2014 at 5:01 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Anna, Fsid is the cross sectionall name without the .long. Best martin Sent via my smartphone, please excuse brevity. Original message From: Anna Jonsson Date:06/04/2014 7:22 AM (GMT-05:00) To: Freesurfer support list Subject: [Freesurfer] free-surfer longitudinal Qdec table Hi, I would like to make my freesurfer longitudinal qdec table for the to use in the lme matlab tools. However, does the fsid need to refer to the longitidunally derived subject; eg XXX.long, or the cross-sectionally derived subject, eg XXX. Im not sure based on the specification online. Kind Regards Anna ___ 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] free-surfer longitudinal Qdec table
Hi, I would like to make my freesurfer longitudinal qdec table for the to use in the lme matlab tools. However, does the fsid need to refer to the longitidunally derived subject; eg XXX.long, or the cross-sectionally derived subject, eg XXX. Im not sure based on the specification online. Kind Regards Anna ___ 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 question
thank you. I have another question; I am getting several significant clusters for group, when correcting for multiple comparisons and total brain size and age, but when I enter sex in, msot of these disappear, but i do not understand whether this is a power issue (as qdec automatically incorporates the interaction effect) or whether this is actually a gender effect? Because the group*gender interaction is non-significant, and the main effect of gender does not have a significant effect of any of the cortical measures either? Please, any help would be greatly appreciated. Kind Wishes, Anna On Mon, May 5, 2014 at 8:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: DOSS is not working in QDEC. It should be disabled in 5.3 doug On 05/05/2014 09:39 AM, Anna Jonsson wrote: Dear group, when using the qdec gui interface, I was wondering where the button or the likes is to change the estimation from its standard doss to dods (different osnet, different slope). I believe I can do this somewhere on the qdec gui without changing to mri_glmfit? ___ 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.
[Freesurfer] qdec question
Dear group, when using the qdec gui interface, I was wondering where the button or the likes is to change the estimation from its standard doss to dods (different osnet, different slope). I believe I can do this somewhere on the qdec gui without changing to mri_glmfit? ___ 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] re finding sulcal folding values
Hi I would like get a mean sulcal folding value per hemisphere and roi data. I have two questions: Is possible do sulcal depth analysis using qdec? And What is the exact command to pass to mris_anatomical_stats to get a mean sulcal depth value /per hemisphere? I have tried some few variations with no luck. Thank you for your help, Kind Wishes, Anna ___ 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] re finding sulcal folding values
hi i think what i meant to write was how to find exact values for sulcal depth? using mris_anatomical_stats, so the exact command that would do this? On Wed, Apr 30, 2014 at 1:32 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Anna at the moment we take the mean out of the sulc before writing it, and use that as kind of the definition of the transition from gyral to sulcal. We can add a switch to mris_inflate to inhibit this behavior if you want I suppose. cheers Bruce On Wed, 30 Apr 2014, Anna Jonsson wrote: Hi I would like get a mean sulcal folding value per hemisphere and roi data. I have two questions: Is possible do sulcal depth analysis using qdec? And What is the exact command to pass to mris_anatomical_stats to get a mean sulcal depth value /per hemisphere? I have tried some few variations with no luck. Thank you for your help, Kind Wishes, Anna ___ 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] lgi for longitudinal scans
thank you. But if the lnog process has already been done and these induviduals already have long directories so to speak, I would just put the lgi flag on as normal but just replace the subject name with the long subject name eg ? recon-all -s _long -localGI Thank you On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter mreu...@nmr.mgh.harvard.eduwrote: Hi Anna, for the image processing, you just add the lgi flag to the regular longitudinal recon-all command recon-all -long .. -lgi for the analysis after that you use the long directories. Best, Martin On Mar 15, 2014, at 10:04 AM, Anna Jonsson ajonsso...@gmail.com wrote: Dear group, If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the normal baseline command on the .long data? thank you, kind wishes Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu 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.
[Freesurfer] lgi for longitudinal scans
Dear group, If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the normal baseline command on the .long data? thank you, kind wishes Anna ___ 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] longitudinal process
Dear Freesurfer experts, I want to know if possible when doing longitudinal stream to put subjects with only one time-point through the processing (eg base and long runs) in order to subsequently use with the Matlab lme tools? Or better is to leave them out and only do those with 2+ times? Thank you Kind Regards, Anna ___ 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] Re global lgi values
Thank you. I have tried to write a script to make this above process automatic but it doesn't work. Any tips on how to make the above process into a script for a number of subjects ? Kind Wishes, Anna On Thu, Nov 14, 2013 at 7:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: I think it would be --parc aparc.pial_lgi doug On 11/14/2013 11:27 AM, Anna Jonsson wrote: Thank you. Can I then use aparcstats2table --subjects --hemi lh --meas thickness --parc lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in 1 tablefile or should I use other command? On Wed, Nov 13, 2013 at 6:59 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: yes and yes On 11/13/2013 12:04 PM, Anna Jonsson wrote: Thank you very much. By second I assume you mean second row? And out of the values on the second row it must be the value 2.9472? Is it headed by Area_mm2 or Mean? And what are the units? Thanks again On Wed, Nov 13, 2013 at 4:56 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: that looks correct. It is the 2nd number you want. The first is for the medial wall (not interesting). You can have it report only for cortex by adding --id 1 doug On 11/13/2013 11:45 AM, Anna Jonsson wrote: Dear list, I have a question about extracting global lgi values/hemisphere. I think I have managed to do it correctly using : mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats (Please let me know if this is not correct) I then get this output ( for each individual) ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 7953 5220.0 Seg 2.4055 0.4052 tel:2.4055%20%20%200.40521.5796 2.9763 1.3967 2 1156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? Thank you very much Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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
[Freesurfer] Re Freesurfer type
Dear list members, I was wondering where in the Freesurfer output the information on which freesurfer version has been used to process scans is located? eg recon-all.log? Thank you, Kind Wishes, Anna ___ 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] Re global lgi values
Thank you. Can I then use aparcstats2table --subjects --hemi lh --meas thickness --parc lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in 1 tablefile or should I use other command? On Wed, Nov 13, 2013 at 6:59 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: yes and yes On 11/13/2013 12:04 PM, Anna Jonsson wrote: Thank you very much. By second I assume you mean second row? And out of the values on the second row it must be the value 2.9472? Is it headed by Area_mm2 or Mean? And what are the units? Thanks again On Wed, Nov 13, 2013 at 4:56 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: that looks correct. It is the 2nd number you want. The first is for the medial wall (not interesting). You can have it report only for cortex by adding --id 1 doug On 11/13/2013 11:45 AM, Anna Jonsson wrote: Dear list, I have a question about extracting global lgi values/hemisphere. I think I have managed to do it correctly using : mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats (Please let me know if this is not correct) I then get this output ( for each individual) ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 7953 5220.0 Seg 2.4055 0.4052 1.5796 2.9763 1.3967 2 1156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? Thank you very much Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto: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. -- 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] Re global lgi values
Dear list, I have a question about extracting global lgi values/hemisphere. I think I have managed to do it correctly using : mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats (Please let me know if this is not correct) I then get this output ( for each individual) ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 7953 5220.0 Seg 2.4055 0.4052 1.5796 2.9763 1.3967 2 1156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? Thank you very much Anna ___ 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] Re global lgi values
Thank you very much. By second I assume you mean second row? And out of the values on the second row it must be the value 2.9472? Is it headed by Area_mm2 or Mean? And what are the units? Thanks again On Wed, Nov 13, 2013 at 4:56 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: that looks correct. It is the 2nd number you want. The first is for the medial wall (not interesting). You can have it report only for cortex by adding --id 1 doug On 11/13/2013 11:45 AM, Anna Jonsson wrote: Dear list, I have a question about extracting global lgi values/hemisphere. I think I have managed to do it correctly using : mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats (Please let me know if this is not correct) I then get this output ( for each individual) ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 7953 5220.0 Seg 2.4055 0.4052 1.5796 2.9763 1.3967 2 1156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? Thank you very much Anna ___ 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: [Gendergap] Topless image retention on Commons and use on enwp
for your good work !! Anna Jonsson Date: Mon, 29 Apr 2013 08:29:40 -0700 From: sarah.stie...@gmail.com To: gendergap@lists.wikimedia.org Subject: Re: [Gendergap] Topless image retention on Commons and use on enwp Sorry if this gets a little off topic from the actual focus of the subjects. I just need to personally vent and this gives me a chance (thanks Katherine). I assume I can't be the only one who feels this way, and it seems you might also. I totally understand the it depresses me situation. I got involved in some of the discussions about the women's foo categories only to get bombarded with comments when I brought up I don't know if anyone here is even a woman involved, from what I know, I think I might be the only woman here, and then to be snapped at How do you know I'm not a woman? by someone with a male user name (Jeremy). I felt like a total fail, and basically left the conversation only to get comments on my talk page. I have officially declared I'm burnt out on any and all gender conversations, specifically triggered by the recent category situation. 95% if not more of the people discussing all of these things are, from what I believe, identifying on Wikipedia as the masculine. It's really troubling for me, and right now I'm at the point where I just can't fight it right now. I'm feeling depressed about it, hopeless, and all of the other fun things that go with burn out. (Funny, I didn't suffer burn out this severe when I was a fellow, but I did have two minor bouts of burn out during that year, this is by far the worst) I basically had to stop doing the painful nomination and arguing about nudity and women's images on Commons. Part of this was because it was so demoralizing and depressing, and the other was the repeated You'll never be an admin on Commons if you keep doing this, and I always wanted to be an admin on Commons. The fact that I let this argument - being made by male Commonists - trigger me to not participate in the conversations is an entirely different psychological issue in itself! Oy vey. Gah. :( -Sarah On Mon, Apr 29, 2013 at 8:08 AM, Katherine Casey fluffernutter.w...@gmail.com wrote: Came across this kerfuffle today. I'd love to see what more gendergap-focused people think about the following progression of events (note: the image is NSFW, but each of the links I'm providing are SFW if you don't click through to the image/article): http://en.wikipedia.org/wiki/Talk:Exhibitionism#Image_at_top_of_page ---discussion about whether to use an identifiable woman's topless photo on the top of an enwp article. The person raising the discussion notes that I find it hard to believe that this woman wants her picture on WP, and I don't think we have a right to show her because of a momentary indiscretion in a public place. http://commons.wikimedia.org/wiki/Commons:Deletion_requests/File:Mardi_Gras_Flashing_-_Color.jpg#File:Mardi_Gras_Flashing_-_Color.jpg ---Same image is nominated for deletion on Commons, with similar rationale The image is kept.Discussion on enwp spins off from the same issue: http://en.wikipedia.org/wiki/Wikipedia:BLPN#Photos_of_private_people_doing_things_they_might_be_embarrassed_about_later , splitting between one faction saying It's legal, so it's fine and another saying It's a matter of ethics, not legality. Speaking personally, my takeaway from reading through this situation has gone through mortification in empathy for the image subject, who was almost certainly drunk and unable to consent, frustration with Commons's dismissive approach to the questioning of identfiable sexual images, and finally realization that in all three discussions, I see no users who I know to be female. Not one. It seems quite likely that the issue of whether this woman's right to be protected by BLP extends to images of her breasts...is being discussed 100% by men. I don't quite know what my point is here, other than to note that to me, this feels very, very representative of the way women and women's issues are treated on WP and on Commons, even when we're supposed to be hyper-aware of the gendergap and its effects, and it depresses me. -Fluffernutter ___ Gendergap mailing list Gendergap@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/gendergap -- -- Sarah Stierch Museumist, open culture advocate, and Wikimedianwww.sarahstierch.com ___ Gendergap mailing list Gendergap@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/gendergap ___ Gendergap mailing list Gendergap@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/gendergap
Re: [Gendergap] Mind the Gap Barnstar/Award - I need your help!
yes, I can see your point,no problem I just wanted to try to contribute with something Anna Date: Tue, 4 Oct 2011 11:39:19 -0400 From: sarah.stie...@gmail.com To: gendergap@lists.wikimedia.org Subject: Re: [Gendergap] Mind the Gap Barnstar/Award - I need your help! Hi Anna - Cool drawing! In my original email I was actually seeking something inspired by the Mind the Gap theme from the London underground. It is a cool drawing - but I do think having something more gender neutral will be ideal for this award (you can learn more about barnstars here: http://en.wikipedia.org/wiki/Wikipedia:Barnstars ). While she has quite the personality (it appears an angry one, and many of us can relate to that!) the vagina vision (ha!) might make it a little odd to give to men and for men to give to others. Thank you for your effort! -Sarah Stierch On Mon, Oct 3, 2011 at 4:10 AM, anna jonsson annaba...@hotmail.com wrote: Hi everyone, I'm an artist,and recently found out about this gendergap list amazing work you have done! so I send a proposal for the logo... Anna Date: Sun, 2 Oct 2011 21:17:38 -0400 From: sarah.stie...@gmail.com To: gendergap@lists.wikimedia.org Subject: [Gendergap] Mind the Gap Barnstar/Award - I need your help! Hi everyone, I recently mentioned the idea of the Mind the Gap barnstar/award. The term mind the gap is in reference to the warning set forth by the London underground to warn people to make sure they pay attention the space between the train door and the station platform (learn more here: http://en.wikipedia.org/wiki/Mind_the_gap). Are you a designer? Or do you know a designer who would be happy to volunteer their time to creating an award for Wikimedians who work hard to close the gap within Wikimedia through outreach, welcoming, standing up for others, writing about and maintaining women's articles or related images, and forth? Here is the original Mind the Gap logo...which I believe is under copyright?: http://www.earthpm.com/wp-content/uploads/2011/06/mind_the_gap.png Here is a cool feminist spin on it: http://londonstudentfeminists.blogspot.com/ Another fun piece of inspiration - the German women's movement logo of the 1970: http://en.wikipedia.org/wiki/File:Womanpower_logo.svg I tried to develop something myself, but, my own skills are rather pathetic in regards to design. I will award you with a barnstar of your own and a beer if I ever meet you (or a beverage of your choice) - or the designer you recruit!! And of course fanatically praise the awesome-ness you or the designer are through Twitter, Wikipedia, mailing lists and beyond.. 3 THANK YOU for your consideration! -Sarah Stierch -- GLAMWIKI Partnership Ambassador for Wikimedia Wikipedian-in-Residence, Archives of American Art and Sarah Stierch Consulting Historical, cultural artistic research advising. -- http://www.sarahstierch.com/ ___ Gendergap mailing list Gendergap@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/gendergap ___ Gendergap mailing list Gendergap@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/gendergap -- GLAMWIKI Partnership Ambassador for Wikimedia Wikipedian-in-Residence, Archives of American Art and Sarah Stierch Consulting Historical, cultural artistic research advising. -- http://www.sarahstierch.com/ ___ Gendergap mailing list Gendergap@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/gendergap ___ Gendergap mailing list Gendergap@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/gendergap
[Gendergap] 86% are white young men
http://youtu.be/tvUSoWVq0_A ___ Gendergap mailing list Gendergap@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/gendergap
