Re: [Freesurfer] Can not visualize read_surf.m output with matlab
Dear Bruce,
I see. I will just shift everything by one.
Thank you!
Sincerely,
Ye
On Wed, Jun 18, 2014 at 9:14 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Our indices are zero based, and matlab is one based. That is probably the
problem
Bruce
On Jun 18, 2014, at 1:09 PM, ye tian tianye...@gmail.com wrote:
Dear Freesurfers,
I tried the following in matlab
[coords,faces] =read_surf('\subject\surf\rh.orig')
Hp = patch('vertices',coords,'faces',faces(:,[1 3 2]),...
'facecolor',[.5 .5 .5],'edgecolor','none')
camlight('headlight','infinite')
vertnormals = get(Hp,'vertexnormals');
Matlab returns the following error:
Error using patch
Faces values must be = 1.0
Indeed, there are 0's in faces. Is this a mistake?
Thank you very much!
Sincerely,
Ye
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Re: [Freesurfer] Linear Mixed Models in FS?
Yes there is numerical instability when p-values becomes extremely low and your solution is OK. You are just being conservative. Your actual p-value might have been 1e-25 but you couldn't observe it exactly (got zero instead) because of numerical limitations of the Matlab's fcdf function. I'll fix this issue on github:https://github.com/NeuroStats this weekend. Best -Jorge De: Lars M. Rimol lari...@gmail.com Para: jorge luis jbernal0...@yahoo.es CC: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Enviado: Jueves 19 de junio de 2014 5:01 Asunto: Re: [Freesurfer] Linear Mixed Models in FS? Hi Jorge, Thank you! Yes this makes sense, because this confirms that the second covariate in fact tests for an effect across all groups, just as I expected. Now, there's another problem with these analyses: Please consider the attached figure lh_model1_01000_interaction_nopatch_lateral.tif, which shows a p-map (cortical area, smoothed with 30 mm fwhm) with two gray regions in the temporal lobe and the insula/IFG in the middle of highly significant regions. There is no darker blue transition into the non-significant regions. These gray regions appear to be artifacts based on eye balling of the maps. I checked the output of the significance testing in those regions and it appears that the output of this formula (in lme_mass_f.m) is extremely low: pval(i) = 1-fcdf(Fstat,szC,m); I assume there may be numerical instability when pval becomes extremely low? Could that explain this? I changed the code so that if 1-fcdf(Fstat,szC,m) is zero or less than 1e-15, then pval(i) = max(1-fcdf(Fstat,szC,m),1e-15); (or, if it's negative pval(i) = min(1-fcdf(Fstat,szC,m),-1e-15) ) If it's not, then the old code applies: pval(i) = 1-fcdf(Fstat,szC,m); This seems to have fixed the problem as the figure model1_area_lh_01000_winteraction_wpatch_lateral.tif shows. Again, based on eye-balling the maps. I have seen this problem in several data sets, both cortical and subcortical data. In all cases using a lower limit for 1-fcdf(Fstat,szC,m) - either 1e-15 or 1e-20 - seems to fix the problem. Do you concur that the problem is numerical instability and is this a good way to fix it? Thank you! yours, LMR On Wed, Jun 18, 2014 at 3:49 PM, jorge luis jbernal0...@yahoo.es wrote: Hi LMR If the interaction term is not statistically significant then there is no evidence of the existence of two different groups in your sample (as far as the longitudinal trajectory is concerned they are all controls, the groups might be different at baseline though). This is why main effects are only tested after the interactions have been previously tested. In your model a common “base time slope” is assumed for both groups (the second coefficient) but you are also explicitly modeling the possibility of the case-group slope being exceeding the control/common base slope by an extra quantity. That quantity is the interaction term. Hope this makes sense Best -Jorge De: Lars M. Rimol lari...@gmail.com Para: FS maling list freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 18 de junio de 2014 8:57 Asunto: Re: [Freesurfer] Linear Mixed Models in FS? Hi Jorge, Thank you for your reply! Again considering the same model from before intercept(random effect) + centered age + group + group x centered age + sex I think what is confusing me is that I think of the [centered age] covariate as a column vector which will contain the centered age of both the control- and the case group. This is how it would be seen in a GLM using the same design matrix. Therefore it is difficult for me to understand how the contrast [0 1 0 0 0] can inform us about the control group alone. To me it would seem obvious that this contrast tells me something about the effect of [centered age] on the whole of the sample, regardless of the group each subject belongs to. On the other hand, I agree with you that the interaction term could tell us something about the effect of [centered age] on the case-group by considering the contrast vector [0 0 0 1 0]. Just for the sake of argument, please consider the following model intercept(random effect) + (1-group) x centered age + group + group x centered age + sex and compare to the one presented above. Here (1-group) is a column vector which is 1 where the [group] vector is 0, and vice versa. This difference ensures that the second term only includes numbers from the control-group. Applying the contrast [0 1 0 0 0] to this model, would this not be more appropriate for consider the effect of [centered age] on the control-group alone? Given your previous answers I suspect I'm missing something here, but I would greatly appreciate if you could please take the time to explain to me how I've gone wrong. Thanks! LMR --- Hi
Re: [Freesurfer] Linear Mixed Models in FS?
Ey! Dice Lilla que estas currando en el Childrens? Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: jorge luis jbernal0...@yahoo.es To: Lars M. Rimol lari...@gmail.com Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 19, 2014 8:56:38 AM Subject: Re: [Freesurfer] Linear Mixed Models in FS? Yes there is numerical instability when p-values becomes extremely low and y our solution is OK. You are just being conservative. Your actual p-value might have been 1e-25 but you couldn't observe it exactly (got zero instead) because of numerical limitations of the Matlab's fcdf function. I'll fix this issue on github: https://github.com/NeuroStats this weekend. Best -Jorge De: Lars M. Rimol lari...@gmail.com Para: jorge luis jbernal0...@yahoo.es CC: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Enviado: Jueves 19 de junio de 2014 5:01 Asunto: Re: [Freesurfer] Linear Mixed Models in FS? Hi Jorge, Thank you! Yes this makes sense, because this confirms that the second covariate in fact tests for an effect across all groups, just as I expected. Now, there's another problem with these analyses: Please consider the attached figure lh_model1_01000_interaction_nopatch_lateral.tif , which shows a p-map (cortical area, smoothed with 30 mm fwhm) with two gray regions in the temporal lobe and the insula/IFG in the middle of highly significant regions. There is no darker blue transition into the non-significant regions. These gray regions appear to be artifacts based on eye balling of the maps. I checked the output of the significance testing in those regions and it appears that the output of this formula (in lme_mass_f.m) is extremely low: pval(i) = 1-fcdf(Fstat,szC,m); I assume there may be numerical instability when pval becomes extremely low? Could that explain this? I changed the code so that if 1-fcdf(Fstat,szC,m) is zero or less than 1e-15, then pval(i) = max(1-fcdf(Fstat,szC,m),1e-15); (or, if it's negative pval(i) = min(1-fcdf(Fstat,szC,m),-1e-15) ) If it's not, then the old code applies: pval(i) = 1-fcdf(Fstat,szC,m); This seems to have fixed the problem as the figure model1_area_lh_01000_winteraction_wpatch_lateral.tif shows. Again, based on eye-balling the maps. I have seen this problem in several data sets, both cortical and subcortical data. In all cases using a lower limit for 1-fcdf(Fstat,szC,m) - either 1e-15 or 1e-20 - seems to fix the problem. Do you concur that the problem is numerical instability and is this a good way to fix it? Thank you! yours, LMR On Wed, Jun 18, 2014 at 3:49 PM, jorge luis jbernal0...@yahoo.es wrote: Hi LMR If the interaction term is not statistically significant then there is no evidence of the existence of two different groups in your sample (as far as the longitudinal trajectory is concerned they are all controls, the groups might be different at baseline though). This is why main effects are only tested after the interactions have been previously tested. In your model a common “base time slope” is assumed for both groups (the second coefficient) but you are also explicitly modeling the possibility of the case-group slope being exceeding the control/common base slope by an extra quantity. That quantity is the interaction term. Hope this makes sense Best -Jorge De: Lars M. Rimol lari...@gmail.com Para: FS maling list freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 18 de junio de 2014 8:57 Asunto: Re: [Freesurfer] Linear Mixed Models in FS? Hi Jorge, Thank you for your reply! Again considering the same model from before intercept(random effect) + centered age + group + group x centered age + sex I think what is confusing me is that I think of the [centered age] covariate as a column vector which will contain the centered age of both the control- and the case group. This is how it would be seen in a GLM using the same design matrix. Therefore it is difficult for me to understand how the contrast [0 1 0 0 0] can inform us about the control group alone. To me it would seem obvious that this contrast tells me something about the effect of [centered age] on the whole of the sample, regardless of the group each subject belongs to. On the other hand, I agree with you that the interaction term could tell us something about the effect of [centered age] on the case-group by considering the contrast vector [0 0 0 1 0]. Just for the sake of argument, please consider the following model intercept(random effect) + (1-group) x centered age + group + group x centered age + sex and compare to the one presented above. Here (1-group) is a column vector which is 1 where the [group] vector is 0, and vice versa. This difference ensures that the second term only
[Freesurfer] Labels to annotation
Dear Freesurfer experts, I have made a parcellation of the white matter surface outside of freesurfer in volumes. I convert the volume labels to surface labels. I have now a lot of surface labels (~500 for each hemisphere) which I want to concatenate to an annotation file for easier visualization. When I use mris_label2annot to perform this operation I get a lot of warnings: WARNING: vertex 6021 maps to multiple labels! (overwriting), and the result does not look right. When I load some of the single labels into freeview or tksurfer they look fine. Does anyone know how to perform this operation? How do I avoid the warnings? I do the operations (volume labels--surface labels--annotation) on each hemisphere separately, but I have some regions located in both hemispheres. Is it then possible to keep the whole region the same color across hemispheres during the operations? Best, Karen ___ 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] problem of Label file
hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a detailed description of how you created the label? This seems like a bug. cheers Bruce On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. 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.
[Freesurfer] mkcontrast weighting a complicated double subtraction contrast
Hi, I’m having trouble figuring out the correct way to weight my conditions with mkcontrast for a couple of complicated contrasts I’m making. I have six conditions: #1 female face approach #2 male face approach #3 female face withdraw #4 male face withdraw #5 car approach #6 car withdraw For a couple of contrasts, I had to manually weight with -wcond. For this first one, everything worked. First I made an all faces (male and female, approaching or withdrawing) v. fixation (face_v_fix) contrast, weighted -a 1 -a 2 -a 3 -a 4. I then made an all cars (approaching or withdrawing) v. fixation (car_v_fix) contrast, weighted -a 5 -a 6. To make my contrast face_v_car, which is a subtraction of the above two contrasts, I used the command: mkcontrast-sess -contrast face_v_car -analysis 5.3loom_objns4runs.lh -ncond 6 -wcond 0.25 0.25 0.25 0.25 -0.5 -0.5. When I extracted the data in an ROI analysis for these three contrasts and a bunch others, I manually checked all ROI values for a given subject. The values for my face_v_fix and car_v_fix are correct, and when I manually subtract those two values, it gives me a value identical to the value that derives from the contrast itself. This is as it should be, as they’re two methods of computing the same thing. My problem is with a similar trio of contrasts. My contrast for all faces (both male and female) approaching minus all faces (male and female) withdrawing (aka face-aw), which is weighted -a 1 -a 2 -c 3 -c 4 in the mkcontrast command, and my car approaching minus car withdrawing contrast (aka car-aw), which is weighted -a 5 -a 6, are both fine. I’m trying to make a contrast face-aw minus car-aw (aka face-aw_v_car-aw), which essentially involves a double subtraction (faces approaching minus faces withdrawing, MINUS cars approaching vs. cars withdrawing) in which the face-aw part involves 4 conditions because of the two genders of faces but the car-aw part involves only 2. The command I used was: mkcontrast-sess -contrast face-aw_v_car-aw -analysis 5.3loom_objsns4runs.lh -ncond 6 -wcond 0.25 0.25 -0.25 -0.25 -0.5 0.5. When I extracted the ROI data, the values for my face-aw and car-aw contrasts were correct, but when I manually subtract them the value is different from the value that derives from the face-aw_v_car-aw contrast itself, when it should be equivalent. I have no idea why it’s not working. The only thing I can think that would affect this and mess it up is my weighting in the mkcontrast command. Do you know if I’m using the wrong weighting numbers or missing a flag I need or if there's some way to configure the contrast differently I should be doing? I’m sorry if I provided way more information than I needed to or not nearly enough; I’m very new at all things FreeSurfer and finding that the learning curve can be challenging. Thanks so much, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078 ___ 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] problem of Label file
Dear Bruce, I creat the file of label according to the manual of free surfer. The website was http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. (1) hold down shift then left click and drag to draw the ROI. (2) save the label by selecting File -- Save Label. Thank you very much. Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午9:45，Bruce Fischl fis...@nmr.mgh.harvard.edu 写道： hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a detailed description of how you created the label? This seems like a bug. cheers Bruce On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. Thank you. 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] problem of Label file
using tksurfer? On what fsaverage? On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: Dear Bruce, I creat the file of label according to the manual of free surfer. The websitewas http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. (1) hold down shift then left click and drag to draw the ROI. (2) save the label by selecting File -- Save Label. Thank you very much. Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午9:45，Bruce Fischl fis...@nmr.mgh.harvard.edu 写道： hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a detailed description of how you created the label? This seems like a bug. cheers Bruce On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. Thank you. 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] problem of Label file
Dear Bruce No, I used QDEC to create label. It should be fsaverage. Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午10:00，Bruce Fischl fis...@nmr.mgh.harvard.edu 写道： using tksurfer? On what fsaverage? On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: Dear Bruce, I creat the file of label according to the manual of free surfer. The websitewas http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. (1) hold down shift then left click and drag to draw the ROI. (2) save the label by selecting File -- Save Label. Thank you very much. Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午9:45，Bruce Fischl fis...@nmr.mgh.harvard.edu 写道： hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a detailed description of how you created the label? This seems like a bug. cheers Bruce On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. Thank you. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem of Label file {Disarmed}
Dear Bruce I used QDEC to create the label. It should be fsaverage. Thank you 2014-06-19 22:04 GMT+08:00 wangkangcheng_gmail kangchengwang0...@gmail.com : Dear Bruce No, I used QDEC to create label. It should be fsaverage. Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午10:00，Bruce Fischl fis...@nmr.mgh.harvard.edu 写道： using tksurfer? On what fsaverage? On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: Dear Bruce, I creat the file of label according to the manual of free surfer. The websitewas http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. (1) hold down shift then left click and drag to draw the ROI. (2) save the label by selecting File -- Save Label. Thank you very much. Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午9:45，Bruce Fischl fis...@nmr.mgh.harvard.edu 写道： hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a detailed description of how you created the label? This seems like a bug. cheers Bruce On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. Thank you. 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. -- Kangcheng Wang Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com/wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 王康程 西南大学心理学部 邮箱：kangchengwang0...@gmail.com/wangkangcheng@163.com 地址：重庆市北碚区天生路2号 邮编:400715 ___ 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] Basename error
Hi all, I am analyzing functional data using fsfast 5.3 with the error: Error using== basename. It seems that the same problem was reported before in the mail list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.html), but I can't find answer in the discussion thread in the above link. Any suggestions? Thanks, Xiaomin Yue ___ 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] Problem with freeview
Dear all, trying to follow the freesurfer longitudinal tutorial I encounter the following problem. Commands I digit in a new shell: ~tcsh ~source $FREESURFER_HOME/SetUpFreeSurfer.csh ~setenv SUBJECTS_DIR freesurfer_tutorial/long-tutorial/ ~cd $SUBJECTS_DIR ~freeview -f OAS2_0001/surf/lh.pial:overlay=OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=OAS2_0001/surf/lh.long.thickness-stack.mgh:annot=OAS2_0001/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale Output: Option 'timecourse' not recognized. Run 'freeview -h' for more information. 1- If I remove the timecourse option together with another 3 the command executes correctly. 2- As output of the bugr command I get: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-64-generic x86_64 Could anybody please telle me what's my problem? Thanks Fabio ___ 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] Problem with freeview
Are you running the dev version of freeview? Ruopeng On 06/19/2014 11:27 AM, Bernardoni, Fabio wrote: Dear all, trying to follow the freesurfer longitudinal tutorial I encounter the following problem. Commands I digit in a new shell: ~tcsh ~source $FREESURFER_HOME/SetUpFreeSurfer.csh ~setenv SUBJECTS_DIR freesurfer_tutorial/long-tutorial/ ~cd $SUBJECTS_DIR ~freeview -f OAS2_0001/surf/lh.pial:overlay=OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=OAS2_0001/surf/lh.long.thickness-stack.mgh:annot=OAS2_0001/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale Output: Option 'timecourse' not recognized. Run 'freeview -h' for more information. 1- If I remove the timecourse option together with another 3 the command executes correctly. 2- As output of the bugr command I get: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-64-generic x86_64 Could anybody please telle me what's my problem? Thanks Fabio ___ 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] Problem with freeview
Hi Fabio, I don't believe the 5.1 version of freeview had that flag. The tutorial instructions are written for 5.3 version of freeview. You can download a more recent version of freeview here (under Other Downloads Info): https://surfer.nmr.mgh.harvard.edu/fswiki/Download You may want to make a backup of your current freeview.bin file. -Louis On Thu, 19 Jun 2014, Bernardoni, Fabio wrote: Dear all, trying to follow the freesurfer longitudinal tutorial I encounter the following problem. Commands I digit in a new shell: ~tcsh ~source $FREESURFER_HOME/SetUpFreeSurfer.csh ~setenv SUBJECTS_DIR freesurfer_tutorial/long-tutorial/ ~cd $SUBJECTS_DIR ~freeview -f OAS2_0001/surf/lh.pial:overlay=OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=OAS2_0001/surf/lh.long.thickness-stack.mgh:annot=OAS2_0001/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale Output: Option 'timecourse' not recognized. Run 'freeview -h' for more information. 1- If I remove the timecourse option together with another 3 the command executes correctly. 2- As output of the bugr command I get: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-64-generic x86_64 Could anybody please telle me what's my problem? Thanks Fabio ___ 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] Seg fault (fwd)
Hi Nick, Thank you so much for your response. Turns out that the XQuartz had updated to 2.7.6, I've reinstalled 2.7.5 and it is working! Finally I can finish this study! Best wishes, Gill _ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain Cognition Lab Beckman Institute University of Illinois, Urbana Email: gillian.e.co...@gmail.commailto:gillian.e.co...@gmail.com gco...@illinois.edumailto:gco...@illinois.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] CSF volume
I see, thanks! 1. No, just add up all the ventricle measures. 2. I think FSL might do this, but you would probably have to mask out the ventricles as I doubt they label sulcal csf separately On Tue, 17 Jun 2014, pfot...@nmr.mgh.harvard.edu wrote: Hi Bruce, Thanks for your reply! I had a couple follow up questions: 1) In order to calculate the total ventricular CSF, should I add the CSF volume reported in the aseg.stats file to the other ventricular volumes or no? 2) Would there be a way to segment the sulcal CSF based on the T2 image? Thanks again for your help, Panos Hi Panos sorry, we don't segment sulcal CSF Bruce On Mon, 16 Jun 2014, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I was wondering whether there is a way to calculate accurately the CSF volume with FreeSurfer (I have both T1 and T2 images). Should I just add the ventricular structures and the CSF volume reported in aseg.stats or is there another way to account for the sulcal CSF based on the T2 and add it to the other volumes? Thanks in advance, Panos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] Basename error
what is your command line and terminal output On 6/19/14 4:36 PM, Xiaomin Yue wrote: Hi all, I am analyzing functional data using fsfast 5.3 with the error: Error using== basename. It seems that the same problem was reported before in the mail list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.html), but I can't find answer in the discussion thread in the above link. Any suggestions? Thanks, Xiaomin Yue ___ 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] mkcontrast weighting a complicated double subtraction contrast
I meant -a 1 -a 2 -c 3 -c 4 for the face-aw contrast On 6/19/14 8:53 PM, Douglas Greve wrote: The face-aw contrast (-a 1 -a 2 -c 1 -c 2) is not doing what you think it is doing. It is implementing 0.5 0.5 -0.5 0.5, so you should divide it by 2 before subtracting car-aw to get the equivalent to fac-aw_v_car-aw doug On 6/19/14 3:57 PM, DeCross, Stephanie N. wrote: Hi, I'm having trouble figuring out the correct way to weight my conditions with mkcontrast for a couple of complicated contrasts I'm making. I have six conditions: #1 female face approach #2 male face approach #3 female face withdraw #4 male face withdraw #5 car approach #6 car withdraw For a couple of contrasts, I had to manually weight with -wcond. For this first one, everything worked. First I made an all faces (male and female, approaching or withdrawing) v. fixation (face_v_fix) contrast, weighted -a 1 -a 2 -a 3 -a 4. I then made an all cars (approaching or withdrawing) v. fixation (car_v_fix) contrast, weighted -a 5 -a 6. To make my contrast face_v_car, which is a subtraction of the above two contrasts, I used the command: mkcontrast-sess -contrast face_v_car -analysis 5.3loom_objns4runs.lh -ncond 6 -wcond 0.25 0.25 0.25 0.25 -0.5 -0.5. When I extracted the data in an ROI analysis for these three contrasts and a bunch others, I manually checked all ROI values for a given subject. The values for my face_v_fix and car_v_fix are correct, and when I manually subtract those two values, it gives me a value identical to the value that derives from the contrast itself. This is as it should be, as they're two methods of computing the same thing. My problem is with a similar trio of contrasts. My contrast for all faces (both male and female) approaching minus all faces (male and female) withdrawing (aka face-aw), which is weighted -a 1 -a 2 -c 3 -c 4 in the mkcontrast command, and my car approaching minus car withdrawing contrast (aka car-aw), which is weighted -a 5 -a 6, are both fine. I'm trying to make a contrast face-aw minus car-aw (aka face-aw_v_car-aw), which essentially involves a double subtraction (faces approaching minus faces withdrawing, MINUS cars approaching vs. cars withdrawing) in which the face-aw part involves 4 conditions because of the two genders of faces but the car-aw part involves only 2. The command I used was: mkcontrast-sess -contrast face-aw_v_car-aw -analysis 5.3loom_objsns4runs.lh -ncond 6 -wcond 0.25 0.25 -0.25 -0.25 -0.5 0.5. When I extracted the ROI data, the values for my face-aw and car-aw contrasts were correct, but when I manually subtract them the value is different from the value that derives from the face-aw_v_car-aw contrast itself, when it should be equivalent. I have no idea why it's not working. The only thing I can think that would affect this and mess it up is my weighting in the mkcontrast command. Do you know if I'm using the wrong weighting numbers or missing a flag I need or if there's some way to configure the contrast differently I should be doing? I'm sorry if I provided way more information than I needed to or not nearly enough; I'm very new at all things FreeSurfer and finding that the learning curve can be challenging. Thanks so much, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078 ___ 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] mkcontrast weighting a complicated double subtraction contrast
The face-aw contrast (-a 1 -a 2 -c 1 -c 2) is not doing what you think it is doing. It is implementing 0.5 0.5 -0.5 0.5, so you should divide it by 2 before subtracting car-aw to get the equivalent to fac-aw_v_car-aw doug On 6/19/14 3:57 PM, DeCross, Stephanie N. wrote: Hi, I’m having trouble figuring out the correct way to weight my conditions with mkcontrast for a couple of complicated contrasts I’m making. I have six conditions: #1 female face approach #2 male face approach #3 female face withdraw #4 male face withdraw #5 car approach #6 car withdraw For a couple of contrasts, I had to manually weight with -wcond. For this first one, everything worked. First I made an all faces (male and female, approaching or withdrawing) v. fixation (face_v_fix) contrast, weighted -a 1 -a 2 -a 3 -a 4. I then made an all cars (approaching or withdrawing) v. fixation (car_v_fix) contrast, weighted -a 5 -a 6. To make my contrast face_v_car, which is a subtraction of the above two contrasts, I used the command: mkcontrast-sess -contrast face_v_car -analysis 5.3loom_objns4runs.lh -ncond 6 -wcond 0.25 0.25 0.25 0.25 -0.5 -0.5. When I extracted the data in an ROI analysis for these three contrasts and a bunch others, I manually checked all ROI values for a given subject. The values for my face_v_fix and car_v_fix are correct, and when I manually subtract those two values, it gives me a value identical to the value that derives from the contrast itself. This is as it should be, as they’re two methods of computing the same thing. My problem is with a similar trio of contrasts. My contrast for all faces (both male and female) approaching minus all faces (male and female) withdrawing (aka face-aw), which is weighted -a 1 -a 2 -c 3 -c 4 in the mkcontrast command, and my car approaching minus car withdrawing contrast (aka car-aw), which is weighted -a 5 -a 6, are both fine. I’m trying to make a contrast face-aw minus car-aw (aka face-aw_v_car-aw), which essentially involves a double subtraction (faces approaching minus faces withdrawing, MINUS cars approaching vs. cars withdrawing) in which the face-aw part involves 4 conditions because of the two genders of faces but the car-aw part involves only 2. The command I used was: mkcontrast-sess -contrast face-aw_v_car-aw -analysis 5.3loom_objsns4runs.lh -ncond 6 -wcond 0.25 0.25 -0.25 -0.25 -0.5 0.5. When I extracted the ROI data, the values for my face-aw and car-aw contrasts were correct, but when I manually subtract them the value is different from the value that derives from the face-aw_v_car-aw contrast itself, when it should be equivalent. I have no idea why it’s not working. The only thing I can think that would affect this and mess it up is my weighting in the mkcontrast command. Do you know if I’m using the wrong weighting numbers or missing a flag I need or if there's some way to configure the contrast differently I should be doing? I’m sorry if I provided way more information than I needed to or not nearly enough; I’m very new at all things FreeSurfer and finding that the learning curve can be challenging. Thanks so much, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078 ___ 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] Retinotopic mapping using selxavg3-sess
Thanks, Doug. I think I've kind of sorted that one out by creating a folder called Retinotopy under freesurfer/subjects/Retinotopy/3/, which contains the 001/, ... 004/ folders containing those their corresponding (polar and eccen) rtopy.par and f.nii files. But now I have another problem. When I run selxavg3-sess -a Retintopy.3.lh -s 3 , it runs up to the point as below, where it's using FSL's BET to Extract Brain. # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_9112/in.nii /tmp/mkbrainmask_9112/brain -m -f 0.1 /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/imtest: not found /usr/local/freesurfer//bin/bet.fsl: 153: [: =: unexpected operator /usr/local/freesurfer//bin/bet.fsl: 231: /usr/local/freesurfer//bin/bet.fsl: /bin/bet2: not found Then I realized that the program looks for those not-found files (remove_ext, imtest, bet2) in /bin/, but actually they're all in /usr/lib/fsl/5.0/. What I did next was to copy those files from /usr/lib/fsl/5.0/ to /bin/, but then I got this error: # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_12619/in.nii /tmp/mkbrainmask_12619/brain -m -f 0.1 /bin/bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory mri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o /tmp/mkbrainmask_12619/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_12619/brain_mask.nii Again, I tried copying the file libfslvtkio.so from /usr/lib/fsl/5.0 to /bin/, but it keeps giving me the same error. So I have two questions: 1) I suspect that selxavg3-sess should be looking for the files in /usr/lib/fsl/5.0 instead of in /bin/. Why does it do that? And how can I direct it to look for files in the former location instead? 2) As a quick fix, is it OK for me to copy all the files from /usr/lib/fsl/5.0 to /bin/? Will it solve the problem? The folder /bin/ contains something else and I don't really feel like messing with it. Many thanks, Alan -- Alan Lee sites.google.com/site/alanlflee/ On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: It looks for it in the current folder. You must run this from the same folder you ran mkanalysis-sess from (which should be your project folder) On 6/17/14 4:13 PM, Alan Lee wrote: Hello, I'm using freesurfer to do retinotopic mapping. I've completed the recon-all, mkanalysis-sess, mri-convert and preproc-sess steps. Now when I run the selxavg3-sess (my subject name is 3): selxavg3-sess -a Retinotopy.3.lh -s 3 I got the following message: ERROR: /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy does not exist It seems to look for a Retintopy folder within /Retinotopy/3/. I suppose the Retinotopy folder should be placed under freesurfer/subjects/ ? Am I missing something here? Any help would be greatly appreciated. Many thanks, Alan = debian:/usr/local/freesurfer/subjects/Retinotopy# selxavg3-sess -a Retinotopy.3.lh -s 3 Surface data self lh -- selxavg3-sess logfile is /usr/local/freesurfer/subjects/Retinotopy/log/selxavg3-sess-Retinotopy-Retinotopy.3.lh-140617154401.log -- preproc-sess -s 3 -d /usr/local/freesurfer/subjects/Retinotopy -a Retinotopy.3.lh -nolog -- preproc-sess logfile is /dev/null -- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ root setenv FREESURFER_HOME /usr/local/freesurfer/ setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/Structural Linux debian 3.2.0-4-486 #1 Debian 3.2.57-3+deb7u1 i686 GNU/Linux /usr/local/freesurfer/subjects/Retinotopy /usr/local/freesurfer//fsfast/bin/preproc-sess -s 3 -d /usr/local/freesurfer/subjects/Retinotopy -a Retinotopy.3.lh -nolog Tue Jun 17 15:44:05 CEST 2014 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain 3 Template - mktemplate-sess -s 3 -d /usr/local/freesurfer/subjects/Retinotopy -fsd Retinotopy -nolog -update Session: /usr/local/freesurfer/subjects/Retinotopy/3 Tue Jun 17 15:44:06 CEST 2014 ERROR: /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy does not exist = -- Alan Lee sites.google.com/site/alanlflee/
Re: [Freesurfer] Segfault error
Jace, If your system auto-updated to XQuartz v2.7.6, which might have happened within the past couple weeks, then you should install v2.7.5 instead, as it seems that another Freesurfer user was able to get tkmedit working again on OSX 10.7.5 after reverting to v2.7.5. N. On Wed, 2014-06-18 at 17:00 -0400, Z K wrote: Hello, Can you please email me the contents of your /Application/freesurfer/build-stamp.txt file? And also what version of OSX you are running by typing sw_vers (without quotes) on the command line? -Zeke On 06/18/2014 01:02 PM, Jace Bradford King wrote: Hello, I am running into a segfault error when trying to use tkmedit or tksufer. I am currently running OSX 10.7.5 and have the most current version of XQuartz installed. Below are the contents of the .xdebug files: .xdebug_tkmedit: tkmedit started: Wed Jun 18 10:58:41 2014 /Applications/freesurfer/tktools/tkmedit.bin bert brainmask.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Users/jaceking Set subject home dir to /Applications/freesurfer/subjects/bert Using interface file /Applications/freesurfer/tktools/tkmedit.tcl Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: .xdebug_tksurfer: Segfault Initializing glut xDebug stack (length: 1) 00: 00: Initializing glut Segfault Initializing glut I also get a Segmentation fault note when trying to launch qdec. Do you have suggestions on how to fix this? Thanks in advance for your assistance. Best, Jace King ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the 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] mkcontrast weighting a complicated double subtraction contrast
I’m not sure if I’m understanding correctly - wouldn’t dividing it by 2 and then subtracting car-aw give me 0.25 0.25 -0.25 -0.25 -0.5 0.5 for the face-aw_v_car-aw contrast, then? That’s what I had tried, and it didn’t work. Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078 On Jun 19, 2014, at 2:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: I meant -a 1 -a 2 -c 3 -c 4 for the face-aw contrast On 6/19/14 8:53 PM, Douglas Greve wrote: The face-aw contrast (-a 1 -a 2 -c 1 -c 2) is not doing what you think it is doing. It is implementing 0.5 0.5 -0.5 0.5, so you should divide it by 2 before subtracting car-aw to get the equivalent to fac-aw_v_car-aw doug On 6/19/14 3:57 PM, DeCross, Stephanie N. wrote: Hi, I’m having trouble figuring out the correct way to weight my conditions with mkcontrast for a couple of complicated contrasts I’m making. I have six conditions: #1 female face approach #2 male face approach #3 female face withdraw #4 male face withdraw #5 car approach #6 car withdraw For a couple of contrasts, I had to manually weight with -wcond. For this first one, everything worked. First I made an all faces (male and female, approaching or withdrawing) v. fixation (face_v_fix) contrast, weighted -a 1 -a 2 -a 3 -a 4. I then made an all cars (approaching or withdrawing) v. fixation (car_v_fix) contrast, weighted -a 5 -a 6. To make my contrast face_v_car, which is a subtraction of the above two contrasts, I used the command: mkcontrast-sess -contrast face_v_car -analysis 5.3loom_objns4runs.lh -ncond 6 -wcond 0.25 0.25 0.25 0.25 -0.5 -0.5. When I extracted the data in an ROI analysis for these three contrasts and a bunch others, I manually checked all ROI values for a given subject. The values for my face_v_fix and car_v_fix are correct, and when I manually subtract those two values, it gives me a value identical to the value that derives from the contrast itself. This is as it should be, as they’re two methods of computing the same thing. My problem is with a similar trio of contrasts. My contrast for all faces (both male and female) approaching minus all faces (male and female) withdrawing (aka face-aw), which is weighted -a 1 -a 2 -c 3 -c 4 in the mkcontrast command, and my car approaching minus car withdrawing contrast (aka car-aw), which is weighted -a 5 -a 6, are both fine. I’m trying to make a contrast face-aw minus car-aw (aka face-aw_v_car-aw), which essentially involves a double subtraction (faces approaching minus faces withdrawing, MINUS cars approaching vs. cars withdrawing) in which the face-aw part involves 4 conditions because of the two genders of faces but the car-aw part involves only 2. The command I used was: mkcontrast-sess -contrast face-aw_v_car-aw -analysis 5.3loom_objsns4runs.lh -ncond 6 -wcond 0.25 0.25 -0.25 -0.25 -0.5 0.5. When I extracted the ROI data, the values for my face-aw and car-aw contrasts were correct, but when I manually subtract them the value is different from the value that derives from the face-aw_v_car-aw contrast itself, when it should be equivalent. I have no idea why it’s not working. The only thing I can think that would affect this and mess it up is my weighting in the mkcontrast command. Do you know if I’m using the wrong weighting numbers or missing a flag I need or if there's some way to configure the contrast differently I should be doing? I’m sorry if I provided way more information than I needed to or not nearly enough; I’m very new at all things FreeSurfer and finding that the learning curve can be challenging. Thanks so much, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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
Re: [Freesurfer] mkcontrast weighting a complicated double subtraction contrast
It should have given you the same thing. I'll have to look more closely when I get back from traveling next week. Please send me an email if I don't get back to you. doug On 6/19/14 10:13 PM, DeCross, Stephanie N. wrote: I’m not sure if I’m understanding correctly - wouldn’t dividing it by 2 and then subtracting car-aw give me 0.25 0.25 -0.25 -0.25 -0.5 0.5 for the face-aw_v_car-aw contrast, then? That’s what I had tried, and it didn’t work. Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078 On Jun 19, 2014, at 2:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I meant -a 1 -a 2 -c 3 -c 4 for the face-aw contrast On 6/19/14 8:53 PM, Douglas Greve wrote: The face-aw contrast (-a 1 -a 2 -c 1 -c 2) is not doing what you think it is doing. It is implementing 0.5 0.5 -0.5 0.5, so you should divide it by 2 before subtracting car-aw to get the equivalent to fac-aw_v_car-aw doug On 6/19/14 3:57 PM, DeCross, Stephanie N. wrote: Hi, I’m having trouble figuring out the correct way to weight my conditions with mkcontrast for a couple of complicated contrasts I’m making. I have six conditions: #1 female face approach #2 male face approach #3 female face withdraw #4 male face withdraw #5 car approach #6 car withdraw For a couple of contrasts, I had to manually weight with -wcond. For this first one, everything worked. First I made an all faces (male and female, approaching or withdrawing) v. fixation (face_v_fix) contrast, weighted -a 1 -a 2 -a 3 -a 4. I then made an all cars (approaching or withdrawing) v. fixation (car_v_fix) contrast, weighted -a 5 -a 6. To make my contrast face_v_car, which is a subtraction of the above two contrasts, I used the command: mkcontrast-sess -contrast face_v_car -analysis 5.3loom_objns4runs.lh -ncond 6 -wcond 0.25 0.25 0.25 0.25 -0.5 -0.5. When I extracted the data in an ROI analysis for these three contrasts and a bunch others, I manually checked all ROI values for a given subject. The values for my face_v_fix and car_v_fix are correct, and when I manually subtract those two values, it gives me a value identical to the value that derives from the contrast itself. This is as it should be, as they’re two methods of computing the same thing. My problem is with a similar trio of contrasts. My contrast for all faces (both male and female) approaching minus all faces (male and female) withdrawing (aka face-aw), which is weighted -a 1 -a 2 -c 3 -c 4 in the mkcontrast command, and my car approaching minus car withdrawing contrast (aka car-aw), which is weighted -a 5 -a 6, are both fine. I’m trying to make a contrast face-aw minus car-aw (aka face-aw_v_car-aw), which essentially involves a double subtraction (faces approaching minus faces withdrawing, MINUS cars approaching vs. cars withdrawing) in which the face-aw part involves 4 conditions because of the two genders of faces but the car-aw part involves only 2. The command I used was: mkcontrast-sess -contrast face-aw_v_car-aw -analysis 5.3loom_objsns4runs.lh -ncond 6 -wcond 0.25 0.25 -0.25 -0.25 -0.5 0.5. When I extracted the ROI data, the values for my face-aw and car-aw contrasts were correct, but when I manually subtract them the value is different from the value that derives from the face-aw_v_car-aw contrast itself, when it should be equivalent. I have no idea why it’s not working. The only thing I can think that would affect this and mess it up is my weighting in the mkcontrast command. Do you know if I’m using the wrong weighting numbers or missing a flag I need or if there's some way to configure the contrast differently I should be doing? I’m sorry if I provided way more information than I needed to or not nearly enough; I’m very new at all things FreeSurfer and finding that the learning curve can be challenging. Thanks so much, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078 ___ 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 mailto: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
[Freesurfer] Decimate surface during recon-all
Hello again. I am still trying to project a label on a decimated surface. I tried to decimate the appropriate surface after recon-all and then to create a new label for this decimated surface, but this doesn't seem to work (see here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36473.html, unfortunately no answer yet). Is there a way to customize the recon-all pipeline, so that every surface that is generated is decimated? I guess, that this would solve the problem. Best regards, Kai ___ 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] mri_label2label results
what version are you using? I think this is a bug we fixed a few months ago. Or another one Bruce On Thu, 19 Jun 2014, Yang, Daniel wrote: Dear all, I found that mri_label2label generates different results, depending on whether the software’s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ 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_label2label results
Dear all, I found that mri_label2label generates different results, depending on whether the software’s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ 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] mri_label2label results
Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013? Thanks, Daniel On 6/19/14, 7:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what version are you using? I think this is a bug we fixed a few months ago. Or another one Bruce On Thu, 19 Jun 2014, Yang, Daniel wrote: Dear all, I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ 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] mri_label2label results
I just tried a few different versions of FreeSurfer. Here are the results: 1. FreeSurfer-5.3 (Linux, CentOS 6, Release: 05/15/2013) 2. FreeSurfer-5.3 (Darwin, Lion, Release: 05/15/2013) 3. FreeSurfer-dev (Linux, CentOS 6, 06/19/2014) 4. FreeSurfer-dev (Darwin, Lion, 06/19/2014) I am comparing the results of mri_label2label and then mris_anatomical_stats here. The results of 3 and 4 are the same The results of 1 and 2 are different The results of 1 and 3 are different The results or 2 and 4 are different In my testing, I used an arbitrary label file and here is detail information of area, volume, thickness, thicknessstd, meancurv, gauscurv, foldind, and curvind 1: 1261.0,4900.0,2.763,0.818,0.145,0.048,28.0,3.7 2: 1109.0,4343.0,2.761,0.798,0.15,0.046,23.0,2.8 3: 1261.0,4900.0,2.763,0.818,0.132,0.032,22.0,2.3 4: 1261.0,4900.0,2.763,0.818,0.132,0.032,22.0,2.3 What should we do here? Is the difference between 1 and 3 trivial? Thanks! Daniel On 6/19/14, 8:13 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013? Thanks, Daniel On 6/19/14, 7:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: what version are you using? I think this is a bug we fixed a few months ago. Or another one Bruce On Thu, 19 Jun 2014, Yang, Daniel wrote: Dear all, I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ 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] mri_label2label results
I think it was a bug we fixed after the release. We can send you new versions on those operating systems and you can try them out. Zeke: can you get Daniel new versions of mri_label2label? thanks Bruce On Fri, 20 Jun 2014, Yang, Daniel wrote: Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013? Thanks, Daniel On 6/19/14, 7:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what version are you using? I think this is a bug we fixed a few months ago. Or another one Bruce On Thu, 19 Jun 2014, Yang, Daniel wrote: Dear all, I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ 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] Control Points ignored
Hi Victor If you upload the subject we will take a look Bruce On Jun 19, 2014, at 1:59 PM, Victor Kovac kovac...@umn.edu wrote: Hello, I have run recon-all on two timepoints of a subject (MPS1011-4 and MPS1011-5). I added control points to MPS1011-4 after the initial recon-all processing because large areas of white matter were excluded. Unfortunately, ~50% of the control points I added were apparently ignored, as they did not cause the missed wm areas to be segmented (see attached images). I have run into this problem in a few other subjects as well, where large wm areas are missed even after adding control points and running recon-all -autorecon2-cp -autorecon3 The other timepoint exited with errors, leaving the brain unsegmented. Any advice on how to accurately analyze these timepoints would be greatly appreciated. Their recon-all logs are also attached. Thank you! Victor MPS1011-4a.png MPS1011-4b.png recon-all.log recon-all.log ___ 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] mri_label2label results
Thanks! Is there a list of bug fixed (after release) somewhere? Should we use the development version instead? Please tell me that it is only mri_label2label that has a bug … On 6/19/14, 9:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: I think it was a bug we fixed after the release. We can send you new versions on those operating systems and you can try them out. Zeke: can you get Daniel new versions of mri_label2label? thanks Bruce On Fri, 20 Jun 2014, Yang, Daniel wrote: Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013? Thanks, Daniel On 6/19/14, 7:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: what version are you using? I think this is a bug we fixed a few months ago. Or another one Bruce On Thu, 19 Jun 2014, Yang, Daniel wrote: Dear all, I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] mri_label2label results
Yes, it was only mri_label2label has that bug On Jun 19, 2014, at 10:14 PM, Yang, Daniel yung-jui.y...@yale.edu wrote: Thanks! Is there a list of bug fixed (after release) somewhere? Should we use the development version instead? Please tell me that it is only mri_label2label that has a bug … On 6/19/14, 9:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I think it was a bug we fixed after the release. We can send you new versions on those operating systems and you can try them out. Zeke: can you get Daniel new versions of mri_label2label? thanks Bruce On Fri, 20 Jun 2014, Yang, Daniel wrote: Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013? Thanks, Daniel On 6/19/14, 7:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what version are you using? I think this is a bug we fixed a few months ago. Or another one Bruce On Thu, 19 Jun 2014, Yang, Daniel wrote: Dear all, I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the 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] Labels to annotation
Hi Karen What do you mean the results don't look right? Can you send an image? Cheers Bruce On Jun 19, 2014, at 9:41 AM, Karen Marie Sandø Ambrosen k...@dtu.dk wrote: Dear Freesurfer experts, I have made a parcellation of the white matter surface outside of freesurfer in volumes. I convert the volume labels to surface labels. I have now a lot of surface labels (~500 for each hemisphere) which I want to concatenate to an annotation file for easier visualization. When I use mris_label2annot to perform this operation I get a lot of warnings: WARNING: vertex 6021 maps to multiple labels! (overwriting), and the result does not look right. When I load some of the single labels into freeview or tksurfer they look fine. Does anyone know how to perform this operation? How do I avoid the warnings? I do the operations (volume labels--surface labels--annotation) on each hemisphere separately, but I have some regions located in both hemispheres. Is it then possible to keep the whole region the same color across hemispheres during the operations? Best, Karen ___ 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] some questions about optseq
Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123 ___ 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] mri_label2label results
That is great to know! I personally feel that there should be some sort of autoupdate function or patch file list in FreeSurfer so that when a bug like this is fixed, FreeSurfer can be updated automatically or we can apply the patch from the website. I think the one currently released should be FreeSurfer 5.3.1, with this bug fixed. This bug could have invalidated the research results to some extent if one is retrieving ROI-based stats manually, I feel. Many major software tend to have bugs after release, like SPSS, so this should be a routine... These are just my two cents. Daniel On Jun 19, 2014, at 10:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Yes, it was only mri_label2label has that bug On Jun 19, 2014, at 10:14 PM, Yang, Daniel yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote: Thanks! Is there a list of bug fixed (after release) somewhere? Should we use the development version instead? Please tell me that it is only mri_label2label that has a bug … On 6/19/14, 9:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: I think it was a bug we fixed after the release. We can send you new versions on those operating systems and you can try them out. Zeke: can you get Daniel new versions of mri_label2label? thanks Bruce On Fri, 20 Jun 2014, Yang, Daniel wrote: Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013? Thanks, Daniel On 6/19/14, 7:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: what version are you using? I think this is a bug we fixed a few months ago. Or another one Bruce On Thu, 19 Jun 2014, Yang, Daniel wrote: Dear all, I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
