Re: [Freesurfer] Paired Analysis Contrasts
External Email - Use Caution Hi Douglas, Thank you so much for your response. We just want to be extra careful about the way we are doing this and so below I have outlined the exact pattern of the group descriptor files we are using along with the contrast. Please let me know if you think this is correct or not. The questions we are asking with this analysis are the same as I outlined in the previous email. *This is our first group descriptor file:* GroupDescriptorFile 1 Title BEIP 8 vs. 16 compare CAU (0) And FCG (1) Class Main Input005_16.long.005Main Input005_8.long.005Main Input006_16.long.006Main Input006_8.long.006Main *This is our second group descriptor file:* GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class cau Class fc Input005_long_pair fc Input006_long_pair cau The contrast to understand group differences in thickness between 8 and 16 yr old data sets are: 1 -1 *Question1:* Is this correct? *Question 2:* If we use the below mentioned way to set up our second group descriptor file, will the above contrasts still work? Or can we use 0 1 contrast with the file below to get at the same thing? We actually ran it both ways and the results weren't similar but I specifically ask this question because we are a little worried about the above 'second group descriptor file' not having a column that says 'Main' and we are trying to understand the right way to do our analyses. *Example group descriptor file 2:* GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class Main Variables group Input005_long_pair Main 1 Input006_long_pair Main 0 Thank you so much! I appreciate all your help with this! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Wed, Nov 14, 2018 at 2:50 PM srishti goel <23srishtig...@gmail.com> wrote: > Hi Douglas, > > Thank you so much for your response. We just want to be extra careful > about the way we are doing this and so below I have outlined the exact > pattern of the group descriptor files we are using along with the contrast. > Please let me know if you think this is correct or not. The questions we > are asking with this analysis are the same as I outlined in the previous > email. > > *This is our first group descriptor file:* > > GroupDescriptorFile 1 > Title BEIP 8 vs. 16 compare CAU (0) And FCG (1) > Class Main > Input005_16.long.005Main > Input005_8.long.005Main > Input006_16.long.006Main > Input006_8.long.006Main > > *This is our second group descriptor file:* > > GroupDescriptorFile 1 > Title BEIP longitudinal Compare CAU (0) And FCG (1) > Class cau > Class fc > Input005_long_pair fc > Input006_long_pair cau > > The contrast to understand group differences in thickness between 8 and 16 > yr old data sets are: > 1 -1 > > *Question1:* Is this correct? > *Question 2:* If we use the below mentioned way to set up our second > group descriptor file, will the above contrasts still work? Or can we use 0 > 1 contrast with the file below to get at the same thing? We actually ran it > both ways and the results weren't similar but I specifically ask this > question because we are a little worried about the above 'second group > descriptor file' not having a column that says 'Main' and we are trying to > understand the right way to do our analyses. > > *Example group descriptor file 2:* > GroupDescriptorFile 1 > Title BEIP longitudinal Compare CAU (0) And FCG (1) > Class Main > Variables group > Input005_long_pair Main 1 > Input006_long_pair Main 0 > > Thank you so much! I appreciate all your help with this! > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > > On Wed, Nov 7, 2018 at 9:24 AM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> >> >> On 10/24/2018 09:45 PM, srishti goel wrote: >> > >> > External Email - Use Caution >> > >> > Hello, >> > >> > I am trying to perform a paired analysis for a data set that has >> > subjects' who belong to either group1 or group2 and have data at time >> > point1 (tp1) and time point2 (tp2). I am following all the steps on >> > the wiki but I want to clarify if the contrasts I plan to use for my >> > analyses are appropriate. >> > >> > For my analyses, I only have two groups and no covariates. I am >> >
Re: [Freesurfer] Paired Analysis Contrasts
External Email - Use Caution Hi Douglas, Thank you so much for your response. We just want to be extra careful about the way we are doing this and so below I have outlined the exact pattern of the group descriptor files we are using along with the contrast. Please let me know if you think this is correct or not. The questions we are asking with this analysis are the same as I outlined in the previous email. *This is our first group descriptor file:* GroupDescriptorFile 1 Title BEIP 8 vs. 16 compare CAU (0) And FCG (1) Class Main Input005_16.long.005Main Input005_8.long.005Main Input006_16.long.006Main Input006_8.long.006Main *This is our second group descriptor file:* GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class cau Class fc Input005_long_pair fc Input006_long_pair cau The contrast to understand group differences in thickness between 8 and 16 yr old data sets are: 1 -1 *Question1:* Is this correct? *Question 2:* If we use the below mentioned way to set up our second group descriptor file, will the above contrasts still work? Or can we use 0 1 contrast with the file below to get at the same thing? We actually ran it both ways and the results weren't similar but I specifically ask this question because we are a little worried about the above 'second group descriptor file' not having a column that says 'Main' and we are trying to understand the right way to do our analyses. *Example group descriptor file 2:* GroupDescriptorFile 1 Title BEIP longitudinal Compare CAU (0) And FCG (1) Class Main Variables group Input005_long_pair Main 1 Input006_long_pair Main 0 Thank you so much! I appreciate all your help with this! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Wed, Nov 7, 2018 at 9:24 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > > > On 10/24/2018 09:45 PM, srishti goel wrote: > > > > External Email - Use Caution > > > > Hello, > > > > I am trying to perform a paired analysis for a data set that has > > subjects' who belong to either group1 or group2 and have data at time > > point1 (tp1) and time point2 (tp2). I am following all the steps on > > the wiki but I want to clarify if the contrasts I plan to use for my > > analyses are appropriate. > > > > For my analyses, I only have two groups and no covariates. I am > > interested to know if the decrease in cortical thickness of subjects > > in group 1 across tp1 and tp2 is more than the decrease in cortical > > thickness of subjects in group 2 across tp1 and tp2. The contrast I > > think should be used for this is: 1 -1. Is that correct? > Yes, if you first take the difference between tp1 and tp2. > > > > I am also interested to know if the cortical thickness decreased for > > subjects regardless of the groups so should I use the contrast: 1 for > > that? > Assuming you are keeping 2 groups, then use > 0.5 0.5 > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> > > skype: srishti.goel12 > > > > > > ___ > > 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] Paired Analysis Contrasts
External Email - Use Caution Hello, I am trying to perform a paired analysis for a data set that has subjects' who belong to either group1 or group2 and have data at time point1 (tp1) and time point2 (tp2). I am following all the steps on the wiki but I want to clarify if the contrasts I plan to use for my analyses are appropriate. For my analyses, I only have two groups and no covariates. I am interested to know if the decrease in cortical thickness of subjects in group 1 across tp1 and tp2 is more than the decrease in cortical thickness of subjects in group 2 across tp1 and tp2. The contrast I think should be used for this is: 1 -1. Is that correct? I am also interested to know if the cortical thickness decreased for subjects regardless of the groups so should I use the contrast: 1 for that? Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Missing files in mri_glm
External Email - Use Caution I understand. Thank you so much! :) Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Mon, Sep 24, 2018 at 12:46 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > I can't remember that far back:), but it would not surprise me if they > were not there in 5.3. You can always use the v6 mri_glmfit with 5.3 data. > > On 09/24/2018 12:39 PM, srishti goel wrote: > > > > External Email - Use Caution > > > > Alright, yes I am using 5.3. What about the efficiency and z files? > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> > > skype: srishti.goel12 > > > > > > > > On Mon, Sep 24, 2018 at 12:36 PM Greve, Douglas N.,Ph.D. > > mailto:dgr...@mgh.harvard.edu>> wrote: > > > > What version of FS are you using? The pcc may only be in the v6. > > > > On 09/24/2018 12:10 PM, srishti goel wrote: > > > > > > External Email - Use Caution > > > > > > Hi, > > > > > > I am running analysis to compare group difference in thickness > > between > > > two groups. I followed all the steps outlined on the wiki: > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > . > > > Everything seemed to work fine except I didn't get the following > > files > > > in each contrast's directory > > > > > > efficiency.dat > > > pcc.mgh > > > z.mgh > > > > > > I don't understand why those files don't show up as I didn't get > > any > > > errors. Any help is appreciated. > > > > > > Best, > > > Srishti > > > Social/Clinical Research Specialist > > > Child Imaging Research and Life Experiences Lab > > > University of North Carolina at Chapel Hill > > > email (W): srish...@email.unc.edu > > <mailto:srish...@email.unc.edu> <mailto:srish...@email.unc.edu > > <mailto:srish...@email.unc.edu>> > > > skype: srishti.goel12 > > > > > > > > > > > > ___ > > > 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 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
Re: [Freesurfer] Missing files in mri_glm
External Email - Use Caution Alright, yes I am using 5.3. What about the efficiency and z files? Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Mon, Sep 24, 2018 at 12:36 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > What version of FS are you using? The pcc may only be in the v6. > > On 09/24/2018 12:10 PM, srishti goel wrote: > > > > External Email - Use Caution > > > > Hi, > > > > I am running analysis to compare group difference in thickness between > > two groups. I followed all the steps outlined on the wiki: > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. > > Everything seemed to work fine except I didn't get the following files > > in each contrast's directory > > > > efficiency.dat > > pcc.mgh > > z.mgh > > > > I don't understand why those files don't show up as I didn't get any > > errors. Any help is appreciated. > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> > > skype: srishti.goel12 > > > > > > > > ___ > > 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] Missing files in mri_glm
External Email - Use Caution Hi, I am running analysis to compare group difference in thickness between two groups. I followed all the steps outlined on the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. Everything seemed to work fine except I didn't get the following files in each contrast's directory efficiency.dat pcc.mgh z.mgh I don't understand why those files don't show up as I didn't get any errors. Any help is appreciated. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fthresh documentation
External Email - Use Caution Thanks a lot Douglas. Does this stand for all commands in freesurfer where we put threshold value such as mri_binarize and mri_vol2surf? Best, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Mon, Jul 16, 2018 at 2:01 PM, Douglas N. Greve wrote: > The values are -log10(p). So if you want to view voxels with p<.01, then > set the threshold = 2 > > > > On 07/05/2018 11:10 PM, srishti goel wrote: > > > > > > Hello, > > > > I am trying to decide what fthresh values should I be using for > > viewing my mkda maps on surface. Where could I find some theoretical > > explanation of how to figure that out the freesurfer wiki? I have read > > a lot of different things on the archive but didn't figure out my answer. > > > > It's great appreciated. > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> > > skype: srishti.goel12 > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] fthresh documentation
External Email - Use Caution Hello, I am trying to decide what fthresh values should I be using for viewing my mkda maps on surface. Where could I find some theoretical explanation of how to figure that out the freesurfer wiki? I have read a lot of different things on the archive but didn't figure out my answer. It's great appreciated. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 ___ 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] fthresh function in tksurfer
External Email - Use Caution Thanks so much Ruopeng Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Jul 5, 2018 at 1:40 PM, Ruopeng Wang wrote: > After you load the label or overlay you should see it on the left panel. > > Best, > Ruopeng > > > On Jul 5, 2018, at 12:54 PM, srishti goel <23srishtig...@gmail.com> wrote: > > External Email - Use Caution > > Hi Rupoeng, > > We downloaded the nightly build for that option but I don't see it coming > on the GUI. I scrolled through every option on the task bar and also the > left panel on the GUI but nothing corresponded to 'z-order'. Could you > please direct me to where exactly should I be looking for this option? > > Thanks, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > On Mon, Jun 11, 2018 at 10:34 AM, Ruopeng Wang > wrote: > >> Yes, I have put an option called z-order in the GUI to control order of >> rendering for overlays, labels and annoations. To use it you will need to >> download and install the nightly build from here: >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview >> >> Best, >> Ruopeng >> >> >> On Jun 9, 2018, at 11:04 AM, srishti goel <23srishtig...@gmail.com> >> wrote: >> >> External Email - Use Caution >> >> Hi Ruopeng, >> >> I just wanted to check and see if there is any update about adding the >> option of changing surface labels to come below overlays in Freeview. >> Thanks! >> >> Best, >> Srishti >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Tue, May 29, 2018 at 2:40 PM, srishti goel <23srishtig...@gmail.com> >> wrote: >> >>> Thanks a lot Ruopeng, really appreciate it. >>> >>> Best, >>> Srishti >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Tue, May 29, 2018 at 10:40 AM, Ruopeng Wang < >>> rpw...@nmr.mgh.harvard.edu> wrote: >>> >>>> It will be added very soon. I'll let you know when it is ready. >>>> >>>> Best, >>>> Ruopeng >>>> >>>> On 05/28/2018 05:35 PM, srishti goel wrote: >>>> >>>> Hi Ruopeng, >>>> >>>> Thank you so much! That option will be super helpful. Are you planning >>>> to add that option to Freeview soon? >>>> >>>> Best, >>>> Srishti >>>> >>>> Best, >>>> Srishti >>>> Social/Clinical Research Specialist >>>> Child Imaging Research and Life Experiences Lab >>>> University of North Carolina at Chapel Hill >>>> email (W): srish...@email.unc.edu >>>> skype: srishti.goel12 >>>> >>>> >>>> On Mon, May 28, 2018 at 2:28 PM, Ruopeng Wang < >>>> rpw...@nmr.mgh.harvard.edu> wrote: >>>> >>>>> Hi Srishti, >>>>> >>>>> In freeview surface labels are always displayed on top of overlays. I >>>>> will add an option to change that. >>>>> >>>>> Best, >>>>> Ruopeng >>>>> >>>>> >>>>> On May 28, 2018, at 9:18 AM, srishti goel <23srishtig...@gmail.com> >>>>> wrote: >>>>> >>>>> Hello, >>>>> >>>>> I did use Freeview but I think using either TkSurfer or Freeview won't >>>>> matter because what I am trying to figure out is what the fthresh value >>>>> means for the map. >>>>> From reading the archive, I understand that, for instance, fthresh >>>>> value of 0.3 will mean that the overlay displays 50% (1/10^3) threshold >>>>> based on intensity/ only voxels which are overlaid by 50% of th
Re: [Freesurfer] fthresh function in tksurfer
External Email - Use Caution Hi Rupoeng, We downloaded the nightly build for that option but I don't see it coming on the GUI. I scrolled through every option on the task bar and also the left panel on the GUI but nothing corresponded to 'z-order'. Could you please direct me to where exactly should I be looking for this option? Thanks, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Mon, Jun 11, 2018 at 10:34 AM, Ruopeng Wang wrote: > Yes, I have put an option called z-order in the GUI to control order of > rendering for overlays, labels and annoations. To use it you will need to > download and install the nightly build from here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview > > Best, > Ruopeng > > > On Jun 9, 2018, at 11:04 AM, srishti goel <23srishtig...@gmail.com> wrote: > > External Email - Use Caution > > Hi Ruopeng, > > I just wanted to check and see if there is any update about adding the > option of changing surface labels to come below overlays in Freeview. > Thanks! > > Best, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > On Tue, May 29, 2018 at 2:40 PM, srishti goel <23srishtig...@gmail.com> > wrote: > >> Thanks a lot Ruopeng, really appreciate it. >> >> Best, >> Srishti >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Tue, May 29, 2018 at 10:40 AM, Ruopeng Wang < >> rpw...@nmr.mgh.harvard.edu> wrote: >> >>> It will be added very soon. I'll let you know when it is ready. >>> >>> Best, >>> Ruopeng >>> >>> On 05/28/2018 05:35 PM, srishti goel wrote: >>> >>> Hi Ruopeng, >>> >>> Thank you so much! That option will be super helpful. Are you planning >>> to add that option to Freeview soon? >>> >>> Best, >>> Srishti >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Mon, May 28, 2018 at 2:28 PM, Ruopeng Wang < >>> rpw...@nmr.mgh.harvard.edu> wrote: >>> >>>> Hi Srishti, >>>> >>>> In freeview surface labels are always displayed on top of overlays. I >>>> will add an option to change that. >>>> >>>> Best, >>>> Ruopeng >>>> >>>> >>>> On May 28, 2018, at 9:18 AM, srishti goel <23srishtig...@gmail.com> >>>> wrote: >>>> >>>> Hello, >>>> >>>> I did use Freeview but I think using either TkSurfer or Freeview won't >>>> matter because what I am trying to figure out is what the fthresh value >>>> means for the map. >>>> From reading the archive, I understand that, for instance, fthresh >>>> value of 0.3 will mean that the overlay displays 50% (1/10^3) threshold >>>> based on intensity/ only voxels which are overlaid by 50% of the subjects. >>>> In my case, the maps are visible at fthresh 0.1 and below but since these >>>> are already thresholded maps from a meta-analysis I am not very clear on >>>> how to interpret the fthresh here. Is it voxels overlaid by ~80% of >>>> studies? >>>> >>>> The other thing I want to figure out is that right now when I view my >>>> overlay with two other labels, the labels (when in solid color and not >>>> outline) cover my overlay. But I would want it the other way round such >>>> that the overlay comes on top of the solid colored labels. Does anyone know >>>> how I can achieve that? >>>> >>>> Thank you so much! >>>> >>>> Best, >>>> Srishti >>>> >>>> Best, >>>> Srishti >>>> Social/Clinical Research Specialist >>>> Child Imaging Research and Life Experiences Lab >>>
Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found
External Email - Use Caution Hello Bruce, As suggested by you, I used tkmeditfv to view the volumetric maps on the surface and it seems like the dACC cluster is lying outside the brain. I checked the registration of the volumetric file using tkregisterfv but surprisingly nothing shows up. I also tried using bbregister and then checked the registration but the same thing happened, the volumetric map doesn't show up in either of those cases. I am confused, as to why that is happening and how can I fix it such that all the clusters are appropriately aligned. The files I am using have been exported from neuroelf program. I exported them as analyze format (.img and .hdr) and then converted it to nifti format using mri_convert. However, with both the analyze and nifti format, similar things happened. Any help is highly appreciated. Thanks, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Tue, Jun 26, 2018 at 11:56 PM, Douglas Greve wrote: > you can try > tkmeditfv subject orig.mgz -surfs -ov clustermap.nii.gz -fminmax .01 3 > you may have to adjust the thresholds (fminmax) > > > On 6/26/18 10:43 PM, srishti goel wrote: > > External Email - Use Caution > Hello Bruce, > > You had mentioned about loading the volumetric maps with the surface to > check that all my clusters are contained within the surfaces. Since I am > very new to freesurfer, could you please guide to where I can find an > appropriate command to do that. > > Thank you so much for all the help! > > Best, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl > wrote: > >> Hi Srishti >> >> you should be able to load the volumetric maps with the surfaces and make >> sure that your clusters are contained within the surface. >> >> cheers >> Bruce >> >> On Mon, 25 Jun 2018, srishti goel wrote: >> >> >>> External Email - Use Caution >>> >>> They are separate clusters not the same clusters but we both of those >>> don't show up when we >>> project the volume maps on surface. Every other cluster comes up and >>> this has happened in >>> about 2-3 files. Are you absolutely sure that the surface in freesurfer >>> includes dACC and >>> insula? >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve >>> wrote: >>> >>> It should be included. But dACC and insula are not close to each >>> other. How can >>> there be a cluster that spans both? >>> >>> >>> On 6/23/18 7:54 PM, srishti goel wrote: >>> >>> External Email - Use Caution >>> >>> Hello, >>> I am using mri_vol2surf to project my volume maps on to the surface. >>> There is a >>> dACC/insula cluster visible in my volume maps that doesn't show up when >>> I project >>> it on the surface. >>> >>> Is that because dACC/insula is not included in surfaces on Freesurfer? >>> >>> Thanks! >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> >>> ___ >>> 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 >>
Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found
External Email - Use Caution Hello Bruce, You had mentioned about loading the volumetric maps with the surface to check that all my clusters are contained within the surfaces. Since I am very new to freesurfer, could you please guide to where I can find an appropriate command to do that. Thank you so much for all the help! Best, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl wrote: > Hi Srishti > > you should be able to load the volumetric maps with the surfaces and make > sure that your clusters are contained within the surface. > > cheers > Bruce > > On Mon, 25 Jun 2018, srishti goel wrote: > > >> External Email - Use Caution >> >> They are separate clusters not the same clusters but we both of those >> don't show up when we >> project the volume maps on surface. Every other cluster comes up and this >> has happened in >> about 2-3 files. Are you absolutely sure that the surface in freesurfer >> includes dACC and >> insula? >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve >> wrote: >> >> It should be included. But dACC and insula are not close to each >> other. How can >> there be a cluster that spans both? >> >> >> On 6/23/18 7:54 PM, srishti goel wrote: >> >> External Email - Use Caution >> >> Hello, >> I am using mri_vol2surf to project my volume maps on to the surface. >> There is a >> dACC/insula cluster visible in my volume maps that doesn't show up when I >> project >> it on the surface. >> >> Is that because dACC/insula is not included in surfaces on Freesurfer? >> >> Thanks! >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ 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_vol2surf: dACC/Insula clusters on surface not found
External Email - Use Caution Hi Bruce, Thank you so much for your prompt help. Can I achieve that with: tkregisterfv --mov [your volume maps] --regheader --s [the subject on whose surface map is registered] --surfs --reg [file name] Best, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl wrote: > Hi Srishti > > you should be able to load the volumetric maps with the surfaces and make > sure that your clusters are contained within the surface. > > cheers > Bruce > > On Mon, 25 Jun 2018, srishti goel wrote: > > >> External Email - Use Caution >> >> They are separate clusters not the same clusters but we both of those >> don't show up when we >> project the volume maps on surface. Every other cluster comes up and this >> has happened in >> about 2-3 files. Are you absolutely sure that the surface in freesurfer >> includes dACC and >> insula? >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve >> wrote: >> >> It should be included. But dACC and insula are not close to each >> other. How can >> there be a cluster that spans both? >> >> >> On 6/23/18 7:54 PM, srishti goel wrote: >> >> External Email - Use Caution >> >> Hello, >> I am using mri_vol2surf to project my volume maps on to the surface. >> There is a >> dACC/insula cluster visible in my volume maps that doesn't show up when I >> project >> it on the surface. >> >> Is that because dACC/insula is not included in surfaces on Freesurfer? >> >> Thanks! >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ 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_vol2surf: dACC/Insula clusters on surface not found
External Email - Use Caution They are separate clusters not the same clusters but we both of those don't show up when we project the volume maps on surface. Every other cluster comes up and this has happened in about 2-3 files. Are you absolutely sure that the surface in freesurfer includes dACC and insula? Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve wrote: > It should be included. But dACC and insula are not close to each other. > How can there be a cluster that spans both? > > On 6/23/18 7:54 PM, srishti goel wrote: > > External Email - Use Caution > Hello, > > I am using mri_vol2surf to project my volume maps on to the surface. There > is a dACC/insula cluster visible in my volume maps that doesn't show up > when I project it on the surface. > > Is that because dACC/insula is not included in surfaces on Freesurfer? > > Thanks! > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found
External Email - Use Caution Hello, I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insula cluster visible in my volume maps that doesn't show up when I project it on the surface. Is that because dACC/insula is not included in surfaces on Freesurfer? Thanks! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 ___ 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] fthresh function in tksurfer
External Email - Use Caution Hi Ruopeng, I just wanted to check and see if there is any update about adding the option of changing surface labels to come below overlays in Freeview. Thanks! Best, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Tue, May 29, 2018 at 2:40 PM, srishti goel <23srishtig...@gmail.com> wrote: > Thanks a lot Ruopeng, really appreciate it. > > Best, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > On Tue, May 29, 2018 at 10:40 AM, Ruopeng Wang > wrote: > >> It will be added very soon. I'll let you know when it is ready. >> >> Best, >> Ruopeng >> >> On 05/28/2018 05:35 PM, srishti goel wrote: >> >> Hi Ruopeng, >> >> Thank you so much! That option will be super helpful. Are you planning to >> add that option to Freeview soon? >> >> Best, >> Srishti >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Mon, May 28, 2018 at 2:28 PM, Ruopeng Wang > > wrote: >> >>> Hi Srishti, >>> >>> In freeview surface labels are always displayed on top of overlays. I >>> will add an option to change that. >>> >>> Best, >>> Ruopeng >>> >>> >>> On May 28, 2018, at 9:18 AM, srishti goel <23srishtig...@gmail.com> >>> wrote: >>> >>> Hello, >>> >>> I did use Freeview but I think using either TkSurfer or Freeview won't >>> matter because what I am trying to figure out is what the fthresh value >>> means for the map. >>> From reading the archive, I understand that, for instance, fthresh value >>> of 0.3 will mean that the overlay displays 50% (1/10^3) threshold based on >>> intensity/ only voxels which are overlaid by 50% of the subjects. In my >>> case, the maps are visible at fthresh 0.1 and below but since these are >>> already thresholded maps from a meta-analysis I am not very clear on how to >>> interpret the fthresh here. Is it voxels overlaid by ~80% of studies? >>> >>> The other thing I want to figure out is that right now when I view my >>> overlay with two other labels, the labels (when in solid color and not >>> outline) cover my overlay. But I would want it the other way round such >>> that the overlay comes on top of the solid colored labels. Does anyone know >>> how I can achieve that? >>> >>> Thank you so much! >>> >>> Best, >>> Srishti >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Fri, May 25, 2018 at 10:09 AM, Douglas Greve >>> wrote: >>> >>>> I don't know anything about neuroelf, but unless your have a binarized >>>> map, then the map is going to change when you change the threshold. BTW, if >>>> you wan to use freeview, you can run tksurferfv with the same args as >>>> tksurfer >>>> >>>> On 5/22/18 3:49 PM, srishti goel wrote: >>>> >>>> >>>> Hello, >>>> >>>> I am trying to view network based maps produced from a meta-analysis >>>> using neuroelf on the surface in freesurfer. The meta-analytic maps are >>>> thresholded maps that represent the proportion of contrasts that activated >>>> at each voxel >>>> >>>> I projected my maps on the surface using: >>>> mri_vol2surf --src negative_allsocial_proportion.img --regheader >>>> mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 >>>> Then to view it used: >>>> tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii >>>> -fthresh 0.05 >>>> The issue I have is with the fthresh value. I read the wiki and some >>>> stuff on archive about the fthresh value but I am unsure what it exa
Re: [Freesurfer] fthresh function in tksurfer
External Email - Use Caution Thanks a lot Ruopeng, really appreciate it. Best, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Tue, May 29, 2018 at 10:40 AM, Ruopeng Wang wrote: > It will be added very soon. I'll let you know when it is ready. > > Best, > Ruopeng > > On 05/28/2018 05:35 PM, srishti goel wrote: > > Hi Ruopeng, > > Thank you so much! That option will be super helpful. Are you planning to > add that option to Freeview soon? > > Best, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > On Mon, May 28, 2018 at 2:28 PM, Ruopeng Wang > wrote: > >> Hi Srishti, >> >> In freeview surface labels are always displayed on top of overlays. I >> will add an option to change that. >> >> Best, >> Ruopeng >> >> >> On May 28, 2018, at 9:18 AM, srishti goel <23srishtig...@gmail.com> >> wrote: >> >> Hello, >> >> I did use Freeview but I think using either TkSurfer or Freeview won't >> matter because what I am trying to figure out is what the fthresh value >> means for the map. >> From reading the archive, I understand that, for instance, fthresh value >> of 0.3 will mean that the overlay displays 50% (1/10^3) threshold based on >> intensity/ only voxels which are overlaid by 50% of the subjects. In my >> case, the maps are visible at fthresh 0.1 and below but since these are >> already thresholded maps from a meta-analysis I am not very clear on how to >> interpret the fthresh here. Is it voxels overlaid by ~80% of studies? >> >> The other thing I want to figure out is that right now when I view my >> overlay with two other labels, the labels (when in solid color and not >> outline) cover my overlay. But I would want it the other way round such >> that the overlay comes on top of the solid colored labels. Does anyone know >> how I can achieve that? >> >> Thank you so much! >> >> Best, >> Srishti >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Fri, May 25, 2018 at 10:09 AM, Douglas Greve >> wrote: >> >>> I don't know anything about neuroelf, but unless your have a binarized >>> map, then the map is going to change when you change the threshold. BTW, if >>> you wan to use freeview, you can run tksurferfv with the same args as >>> tksurfer >>> >>> On 5/22/18 3:49 PM, srishti goel wrote: >>> >>> >>> Hello, >>> >>> I am trying to view network based maps produced from a meta-analysis >>> using neuroelf on the surface in freesurfer. The meta-analytic maps are >>> thresholded maps that represent the proportion of contrasts that activated >>> at each voxel >>> >>> I projected my maps on the surface using: >>> mri_vol2surf --src negative_allsocial_proportion.img --regheader >>> mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 >>> Then to view it used: >>> tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii >>> -fthresh 0.05 >>> The issue I have is with the fthresh value. I read the wiki and some >>> stuff on archive about the fthresh value but I am unsure what it exactly >>> means and does. My issue is that the display of my maps changes when I >>> change the fthresh value even though the maps have been k-thresholded using >>> neuroelf before exporting them to freesurfer. More area is marked up when I >>> decrease the threshold value from 0.1 to 0.05 and nothing is visible above >>> 0.1 >>> >>> Does anyone have any thoughts about what might be going on there and how >>> I can fix it? >>> Do I need to do something totally different from what I am doing? >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> >>>
Re: [Freesurfer] fthresh function in tksurfer
External Email - Use Caution Hi Ruopeng, Thank you so much! That option will be super helpful. Are you planning to add that option to Freeview soon? Best, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Mon, May 28, 2018 at 2:28 PM, Ruopeng Wang wrote: > Hi Srishti, > > In freeview surface labels are always displayed on top of overlays. I will > add an option to change that. > > Best, > Ruopeng > > > On May 28, 2018, at 9:18 AM, srishti goel <23srishtig...@gmail.com> wrote: > > Hello, > > I did use Freeview but I think using either TkSurfer or Freeview won't > matter because what I am trying to figure out is what the fthresh value > means for the map. > From reading the archive, I understand that, for instance, fthresh value > of 0.3 will mean that the overlay displays 50% (1/10^3) threshold based on > intensity/ only voxels which are overlaid by 50% of the subjects. In my > case, the maps are visible at fthresh 0.1 and below but since these are > already thresholded maps from a meta-analysis I am not very clear on how to > interpret the fthresh here. Is it voxels overlaid by ~80% of studies? > > The other thing I want to figure out is that right now when I view my > overlay with two other labels, the labels (when in solid color and not > outline) cover my overlay. But I would want it the other way round such > that the overlay comes on top of the solid colored labels. Does anyone know > how I can achieve that? > > Thank you so much! > > Best, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > On Fri, May 25, 2018 at 10:09 AM, Douglas Greve > wrote: > >> I don't know anything about neuroelf, but unless your have a binarized >> map, then the map is going to change when you change the threshold. BTW, if >> you wan to use freeview, you can run tksurferfv with the same args as >> tksurfer >> >> On 5/22/18 3:49 PM, srishti goel wrote: >> >> >> Hello, >> >> I am trying to view network based maps produced from a meta-analysis >> using neuroelf on the surface in freesurfer. The meta-analytic maps are >> thresholded maps that represent the proportion of contrasts that activated >> at each voxel >> >> I projected my maps on the surface using: >> mri_vol2surf --src negative_allsocial_proportion.img --regheader >> mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 >> Then to view it used: >> tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii >> -fthresh 0.05 >> The issue I have is with the fthresh value. I read the wiki and some >> stuff on archive about the fthresh value but I am unsure what it exactly >> means and does. My issue is that the display of my maps changes when I >> change the fthresh value even though the maps have been k-thresholded using >> neuroelf before exporting them to freesurfer. More area is marked up when I >> decrease the threshold value from 0.1 to 0.05 and nothing is visible above >> 0.1 >> >> Does anyone have any thoughts about what might be going on there and how >> I can fix it? >> Do I need to do something totally different from what I am doing? >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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
Re: [Freesurfer] fthresh function in tksurfer
External Email - Use Caution Hello, I did use Freeview but I think using either TkSurfer or Freeview won't matter because what I am trying to figure out is what the fthresh value means for the map. From reading the archive, I understand that, for instance, fthresh value of 0.3 will mean that the overlay displays 50% (1/10^3) threshold based on intensity/ only voxels which are overlaid by 50% of the subjects. In my case, the maps are visible at fthresh 0.1 and below but since these are already thresholded maps from a meta-analysis I am not very clear on how to interpret the fthresh here. Is it voxels overlaid by ~80% of studies? The other thing I want to figure out is that right now when I view my overlay with two other labels, the labels (when in solid color and not outline) cover my overlay. But I would want it the other way round such that the overlay comes on top of the solid colored labels. Does anyone know how I can achieve that? Thank you so much! Best, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Fri, May 25, 2018 at 10:09 AM, Douglas Greve <dgr...@mgh.harvard.edu> wrote: > I don't know anything about neuroelf, but unless your have a binarized > map, then the map is going to change when you change the threshold. BTW, if > you wan to use freeview, you can run tksurferfv with the same args as > tksurfer > > On 5/22/18 3:49 PM, srishti goel wrote: > > > Hello, > > I am trying to view network based maps produced from a meta-analysis using > neuroelf on the surface in freesurfer. The meta-analytic maps are > thresholded maps that represent the proportion of contrasts that activated > at each voxel > > I projected my maps on the surface using: > mri_vol2surf --src negative_allsocial_proportion.img --regheader > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 > Then to view it used: > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii > -fthresh 0.05 > The issue I have is with the fthresh value. I read the wiki and some stuff > on archive about the fthresh value but I am unsure what it exactly means > and does. My issue is that the display of my maps changes when I change the > fthresh value even though the maps have been k-thresholded using neuroelf > before exporting them to freesurfer. More area is marked up when I decrease > the threshold value from 0.1 to 0.05 and nothing is visible above 0.1 > > Does anyone have any thoughts about what might be going on there and how I > can fix it? > Do I need to do something totally different from what I am doing? > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] fthresh function in tksurfer
External Email - Use Caution Hello, I am trying to view network based maps produced from a meta-analysis using neuroelf on the surface in freesurfer. The meta-analytic maps are thresholded maps that represent the proportion of contrasts that activated at each voxel I projected my maps on the surface using: mri_vol2surf --src negative_allsocial_proportion.img --regheader mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 Then to view it used: tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii -fthresh 0.05 The issue I have is with the fthresh value. I read the wiki and some stuff on archive about the fthresh value but I am unsure what it exactly means and does. My issue is that the display of my maps changes when I change the fthresh value even though the maps have been k-thresholded using neuroelf before exporting them to freesurfer. More area is marked up when I decrease the threshold value from 0.1 to 0.05 and nothing is visible above 0.1 Does anyone have any thoughts about what might be going on there and how I can fix it? Do I need to do something totally different from what I am doing? Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 ___ 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] Projecting meta-analytic map on the surface
External Email - Use Caution Hello Freesurfers, I have a network based map that has been produced from a meta analysis using NeuroElf on the standard colins template. I want to project this map on the surface of an MNI template. Does anyone have thoughts about how that could be achieved? Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 ___ 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_vol2surf: issue with registration
Hi , I am facing an issue when I try to compare two network-based maps, one of which has been registered on a surface while the other one has not. If anyone has tried doing something similar and has any thoughts about it please share your suggestions, I highly appreciate it. I have two sets of network based maps (both generated from meta-analysis), one set is ours' and one set is our collaborators'. We want to compare the two sets of maps. Our collaborators maps are on the surface in freesurfer. We wanted to project our volume based maps on that surface. Our collaborators' maps are: SN_like_cortical_lh.nii SN_like_cortical_rh.nii SN_like_subcortical.nii Our maps are: negative_allsocial_proportion.nii negative_somesocial_proportion.nii Etc. In order to compare their volume map (SN_like_subcortical.nii) to our (negative_allsocial_proportion.nii) we just used the MNI152 template from freesurfer wiki and viewed it in Freeview and it worked fine. The issue is when we try to project our maps on the surface that they used. The gave us the template brain (mni152_subject) folder that had been recon-all already and I just used that with the following steps: mri_vol2surf --src negative_allsocial_proportion.nii --regheader mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 To view it: tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 When I view it, our map doesn't show up on the surface and that is because our map didn't register with --regheader. I checked the registration by using: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --surfs The registration is definitely off, we used bbregister to register our maps on the mni152_subject but that didn't work either. Does anyone has thoughts about this? Thanks! ___ 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_vol2surf: unable to compare volume maps
Yeah, I am unsure where to go from here as well. So the results can be viewed in SPM and on the MNI template space itself, since SPM typically does not have a problem showing multiple images in different sizes. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Apr 12, 2018 at 10:11 AM, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > When you use bbregister, it is expecting the input nii file to represent > the actual anatomy of the subject, so it does not surprise me that it > does not work that well. I'm not sure what to do about this because a > meta analysis image will never have decent anatomy. In theory, it should > be already in alignment with the mni152, but this is trickier than it > seems. How do you usually view the results? In FSL or SPM? Do you view > them on an anatomical image? > > > On 04/12/2018 09:03 AM, srishti goel wrote: > > Hi Douglas, > > > > The negative_allsocial_proportion.nii file has actually been converted > > from a vmp file - 'negative_allsocial.vmp'. We used neruoelf to > > convert the vmp file, option - 'export to analze' and 'export to > > nifti'. The original vmp file represent the results of a meta-analysis. > > > > Let me know if that helps or you would need more information. > > > > Thanks! > > > > Best, > > Srishti > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> > > skype: srishti.goel12 > > > > > > On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > > > how was negative_allsocial_proportion.nii created? > > > > > > On 4/11/18 9:14 PM, srishti goel wrote: > >> Hi, > >> > >> I used bbregister to register: > >> bbregister --mov negative_allsocial_proportion.nii --s > >> mni152_subject --bold --lta register.lta > >> and then viewed it using: > >> tkregisterfv --mov negative_allsocial_proportion.nii --reg > >> register.lta --surfs > >> It doesn't look great but it still looks okay (Screenshot attached). > >> Then I also used lta in tkregisterfv, as: > >> tkregisterfv --mov negative_allsocial_proportion.nii --reg > >> register.lta --s mni152_subject --surfs --reg reg.deleteme.dat > >> In this file, the volume map still lies outside the surface. > >> Could you please help me resolve this issue. > >> I tried using register.lta file in the mri_vol2surf but the > >> overlay map doesn't show up again. > >> Thanks! > >> > >> Best, > >> Srishti > >> Social/Clinical Research Specialist > >> Child Imaging Research and Life Experiences Lab > >> University of North Carolina at Chapel Hill > >> email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> > >> skype: srishti.goel12 > >> > >> > >> On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve > >> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > >> > >> don't use --init-rr ( you don't need to spec an init in > >> version 6) > >> > >> > >> On 4/10/18 9:48 PM, srishti goel wrote: > >>> When I run bbregister, it gives me an error. Attached is the > >>> register.dat.log file for it. > >>> Error: > >>> > >>> reading source './tmp.bbregister.91068/template.nii'... > >>> > >>> mri_robust_register.bin: only pass single frame MRI source > >>> ./tmp.bbregister.91068/template.nii. > >>> > >>> > >>> No such file or directory > >>> > >>> > >>> Any help is greatly appreciated! > >>> > >>> > >>> Best, > >>> Srishti > >>> Social/Clinical Research Specialist > >>> Child Imaging Research and Life Experiences Lab > >>> University of North Carolina at Chapel Hill > >>> email (W): srish...@email.unc.edu > >>> <mailto:s
Re: [Freesurfer] mri_vol2surf: unable to compare volume maps
When I run bbregister, it gives me an error. Attached is the register.dat.log file for it. Error: reading source './tmp.bbregister.91068/template.nii'... mri_robust_register.bin: only pass single frame MRI source ./tmp.bbregister.91068/template.nii. No such file or directory Any help is greatly appreciated! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve <dgr...@mgh.harvard.edu> wrote: > They are not in registration. Try running bbregister to create a > registration file (lta), then pass the lta to tkregisterfv instead of > --regheader > > On 4/9/18 11:49 PM, Bruce Fischl wrote: > > How did you generate the registration? And give us the details of what you > are trying to register > Cheers > Bruce > > On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtig...@gmail.com> wrote: > > Hi Bruce, > > Thanks so much for pointing that out, I totally missed that part. > > Also, the registration definitely isn't appropriate. > Could someone please guide me how to correct this problem. I have attached > a screenshot of how it looks like currently. > > > > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > >> Hi Srishti >> >> the directory you are in doesn't matter. YOu either need to set >> SUBJECTS_DIR in the environment, or use --sd to specify the >> directory that contains your subjects. I think you can also give it the >> full path to a target volume if you want, but maybe Doug can comment as he >> knows this stuff better than I do >> >> cheers >> Bruce >> >> >> >> On Sun, 8 Apr 2018, srishti goel wrote: >> >> When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii >>> --regheader --s >>> mni152_subject --surfs --reg reg.deleteme.dat >>> >>> It gives me the error: cannot find mni152_subject. >>> Although I clearly checked that the directory from which I am submitting >>> this command has the >>> mni152_subject directory within which there are all the other required >>> directories such as: mri, >>> stats, surf, scripts, etc. >>> >>> I am unsure what is happening here. >>> >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve < >>> dgr...@mgh.harvard.edu> wrote: >>> Those commands look ok. My suspicion goes to the use of >>> --regheader. See >>> whether the registration is ok with >>> >>> tkregisterfv --mov negative_allsocial_proportion.nii --regheader >>> --s >>> mni152_subject --surfs --reg reg.deleteme.dat >>> >>> >>> On 04/05/2018 08:34 AM, srishti goel wrote: >>> > Hi, >>> > >>> > I am trying to compare my volume maps >>> > (negative_allsocial_proportion.nii) to someone else's >>> > (SN_like_cortical_lh.nii.gz) who have it on a surface >>> > (mni152_subject). So I used the steps for mri_vol2surf command as >>> > follows: >>> > >>> > Commands: >>> > mri_vol2surf --src negative_allsocial_proportion.nii --regheader >>> > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac >>> 0.5 >>> > Then to view it: >>> > tksurfer mni152_subject lh inflated -overlay >>> ./neg_allsocial_lh.nii >>> > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 >>> > >>> > Everything ran fine and we didn't get any error but then while >>> viewing >>> > the files we could not see our map (neg_allsocail_lh.nii) on the >>> > surface. This file seemed to work fine as it is not an empty >>> file when >>> > I checked the file size. However, when we view it using tksurfer >>> it >>>
Re: [Freesurfer] mri_vol2surf: unable to compare volume maps
When I type this command: tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc. I am unsure what is happening here. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > Those commands look ok. My suspicion goes to the use of --regheader. See > whether the registration is ok with > > tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s > mni152_subject --surfs --reg reg.deleteme.dat > > > On 04/05/2018 08:34 AM, srishti goel wrote: > > Hi, > > > > I am trying to compare my volume maps > > (negative_allsocial_proportion.nii) to someone else's > > (SN_like_cortical_lh.nii.gz) who have it on a surface > > (mni152_subject). So I used the steps for mri_vol2surf command as > > follows: > > > > Commands: > > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 > > Then to view it: > > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii > > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 > > > > Everything ran fine and we didn't get any error but then while viewing > > the files we could not see our map (neg_allsocail_lh.nii) on the > > surface. This file seemed to work fine as it is not an empty file when > > I checked the file size. However, when we view it using tksurfer it > > does not show up as a highlighted portion on the surface. The > > SN_like_cortical_lh.nii.gz file shows up just fine. > > > > Could someone please help me figure out what might have gone wrong here. > > > > Thanks so much! > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)
So it gave this error: 3d normalization pass 1 of 2 white matter peak found at 110 HISTOalloc(-2147483648): could not allocate histogram Cannot allocate memory Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > let's see if it works. If it does, you should be able to run > > recon-all -s SUBJID -make all > > > cheers > Bruce > > > On Thu, 5 Apr 2018, srishti goel wrote: > > Should I re-run the recon-all after running the last command from >> recon-all.cmd? >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Srishti >> >> if you look in the subject's scripts dir there should be a file >> named "recon-all.cmd". Try rerunning the last >> command in it (probably from the mri dir) >> >> cheers >> Bruce >> On Thu, 5 Apr 2018, srishti goel wrote: >> >> I am sorry, I am not sure what do you mean by running the >> command line directly? >> I use the following command: >> >> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user >> srish...@email.unc.edu --wrap "export >> >> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; >> recon-all -s 13166 >> -autorecon2-cp -autorecon3 -nowmsa" >> >> >> where sbatch. until export is our local server submission >> command and I run this command from the >> command line itself, not >> using any script. >> >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> if you run the command that failed again on the command >> line directly (that is, not in >> recon-all) does it fail >> again? >> >> On Thu, 5 Apr 2018, srishti goel wrote: >> >> Hi Bruce, >> >> The machine definitely hasn't run out of memory. >> Here is the memory usage >> from recon-all.log >> >> total used >>free >> shared buff/cache available >> Mem: 26372696834330048 152102696 >> 1294477294224 >> 191963372 >> Swap: 2097148 0 >> 2097148 >> >> >> >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Srishti >> >> are you sure that your machine didn't just >> run out of memory? >> The recon-all.log file includes the amount >> of free (and total) >> memory at the time the process was started. >> >> cheers >> Bruce >> >>On Thu, 5 Apr 2018, srishti goel wrote: >> >> Hi, >> I have been trying to edit structural >> brains and >>
Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)
Should I re-run the recon-all after running the last command from recon-all.cmd? Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Srishti > > if you look in the subject's scripts dir there should be a file named > "recon-all.cmd". Try rerunning the last command in it (probably from the > mri dir) > > > cheers > Bruce > On Thu, 5 Apr 2018, srishti goel wrote: > > I am sorry, I am not sure what do you mean by running the command line >> directly? >> I use the following command: >> >> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user >> srish...@email.unc.edu --wrap "export >> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; >> recon-all -s 13166 -autorecon2-cp -autorecon3 -nowmsa" >> >> >> where sbatch. until export is our local server submission command and >> I run this command from the command line itself, not >> using any script. >> >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> if you run the command that failed again on the command line >> directly (that is, not in recon-all) does it fail >> again? >> >> On Thu, 5 Apr 2018, srishti goel wrote: >> >> Hi Bruce, >> >> The machine definitely hasn't run out of memory. Here is the >> memory usage >> from recon-all.log >> >> total usedfree >> >> shared buff/cache available >> Mem: 26372696834330048 152102696 12944 >> 77294224 >> 191963372 >> Swap: 2097148 0 2097148 >> >> >> >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Srishti >> >> are you sure that your machine didn't just run out of >> memory? >> The recon-all.log file includes the amount of free (and >> total) >> memory at the time the process was started. >> >> cheers >> Bruce >> >>On Thu, 5 Apr 2018, srishti goel wrote: >> >> Hi, >> I have been trying to edit structural brains and >> very few times I would get the following error >> while >> running recon-all -s >> subjID >> >> white matter peak found at 110 >> cannot allocate memory >> >> Upon looking at the archive, there was only one >> similar issue and it was recommend to check >> mri_info >> as the brain mask might >> have been corrupted. I did that and here is the >> output: >> >> Volume information for brainmask.mgz >> >> type: MGH >> >> dimensions: 256 x 256 x 256 >> >>voxel sizes: 1.00, 1.00, 1.00 >> >> type: UCHAR (0) >> >>fov: 256.000 >> >>dof: 0 >> >> xstart: -128.0, xend: 128.0 >> >> ystart: -128.0, yend: 128.0 >> >> zstart: -128.0, zend: 128.0 >> >>
Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)
I am sorry, I am not sure what do you mean by running the command line directly? I use the following command: sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user srish...@email.unc.edu --wrap "export SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; recon-all -s 13166 -autorecon2-cp -autorecon3 -nowmsa" where sbatch. until export is our local server submission command and I run this command from the command line itself, not using any script. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > if you run the command that failed again on the command line directly > (that is, not in recon-all) does it fail again? > > > On Thu, 5 Apr 2018, srishti goel wrote: > > Hi Bruce, >> >> The machine definitely hasn't run out of memory. Here is the memory usage >> from recon-all.log >> >> total usedfree >> shared buff/cache available >> Mem: 26372696834330048 152102696 1294477294224 >> 191963372 >> Swap: 2097148 0 2097148 >> >> >> >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> > >> wrote: >> Hi Srishti >> >> are you sure that your machine didn't just run out of memory? >> The recon-all.log file includes the amount of free (and total) >> memory at the time the process was started. >> >> cheers >> Bruce >> >>On Thu, 5 Apr 2018, srishti goel wrote: >> >> Hi, >> I have been trying to edit structural brains and >> very few times I would get the following error while >> running recon-all -s >> subjID >> >> white matter peak found at 110 >> cannot allocate memory >> >> Upon looking at the archive, there was only one >> similar issue and it was recommend to check mri_info >> as the brain mask might >> have been corrupted. I did that and here is the >> output: >> >> Volume information for brainmask.mgz >> >> type: MGH >> >> dimensions: 256 x 256 x 256 >> >>voxel sizes: 1.00, 1.00, 1.00 >> >> type: UCHAR (0) >> >>fov: 256.000 >> >>dof: 0 >> >> xstart: -128.0, xend: 128.0 >> >> ystart: -128.0, yend: 128.0 >> >> zstart: -128.0, zend: 128.0 >> >> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 >> msec, flip angle: 0.00 degrees >> >>nframes: 1 >> >>PhEncDir: UNKNOWN >> >>FieldStrength: 0.00 >> >> ras xform present >> >> xform info: x_r = -1., y_r = 0., z_r >> = 0., c_r =-1. >> >> : x_a = 0., y_a = 0., z_a >> = 1., c_a =37.5000 >> >> : x_s = 0., y_s = -1., z_s >> = 0., c_s = 4.7185 >> >> >> talairach xfm :/pine/scr/s/r/srishtig/Duke_T >> est/Freesurfer_out/11039/mri/transforms/talair >> ach.xfm >> >> Orientation : LIA >> >> Primary Slice Direction: coronal >> >> >> voxel to ras transform: >> >>-1. 0. 0. 127. >> >> 0. 0. 1. -90.5000 >> >> 0. -1. 0. 132.7185 >> >> 0. 0. 0. 1. >> >> >> voxel-to-ras determinant -1 >> >> >> ras to voxel transform: >> >>
Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)
Hi Bruce, The machine definitely hasn't run out of memory. Here is the memory usage from recon-all.log total usedfree shared buff/cache available Mem: 26372696834330048 152102696 1294477294224 191963372 Swap: 2097148 0 2097148 Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Srishti > > are you sure that your machine didn't just run out of memory? The > recon-all.log file includes the amount of free (and total) memory at the > time the process was started. > > cheers > Bruce > > > On Thu, 5 Apr 2018, srishti goel wrote: > > Hi, >> I have been trying to edit structural brains and very few times I would >> get the following error while running recon-all -s >> subjID >> >> white matter peak found at 110 >> cannot allocate memory >> >> Upon looking at the archive, there was only one similar issue and it was >> recommend to check mri_info as the brain mask might >> have been corrupted. I did that and here is the output: >> >> Volume information for brainmask.mgz >> >> type: MGH >> >> dimensions: 256 x 256 x 256 >> >>voxel sizes: 1.00, 1.00, 1.00 >> >> type: UCHAR (0) >> >>fov: 256.000 >> >>dof: 0 >> >> xstart: -128.0, xend: 128.0 >> >> ystart: -128.0, yend: 128.0 >> >> zstart: -128.0, zend: 128.0 >> >> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 >> degrees >> >>nframes: 1 >> >>PhEncDir: UNKNOWN >> >>FieldStrength: 0.00 >> >> ras xform present >> >> xform info: x_r = -1., y_r = 0., z_r = 0., c_r = >> -1. >> >> : x_a = 0., y_a = 0., z_a = 1., c_a = >> 37.5000 >> >> : x_s = 0., y_s = -1., z_s = 0., c_s = >> 4.7185 >> >> >> talairach xfm : /pine/scr/s/r/srishtig/Duke_Te >> st/Freesurfer_out/11039/mri/transforms/talairach.xfm >> >> Orientation : LIA >> >> Primary Slice Direction: coronal >> >> >> voxel to ras transform: >> >>-1. 0. 0. 127. >> >> 0. 0. 1. -90.5000 >> >> 0. -1. 0. 132.7185 >> >> 0. 0. 0. 1. >> >> >> voxel-to-ras determinant -1 >> >> >> ras to voxel transform: >> >>-1. -0. -0. 127. >> >>-0. -0. -1. 132.7185 >> >>-0. 1. -0.90.5000 >> >>-0. -0. -0. 1. >> >> >> Is there any other way to resolve this issue than reconstruction the >> brain again and doing all the edits all over again hoping >> that the brain mask does not get corrupted this time? >> >> Appreciate any help with this. >> >> Best, >> Srishti >> >> > ___ > 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] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)
Hi, I have been trying to edit structural brains and very few times I would get the following error while running recon-all -s subjID white matter peak found at 110 cannot allocate memory Upon looking at the archive, there was only one similar issue and it was recommend to check mri_info as the brain mask might have been corrupted. I did that and here is the output: Volume information for brainmask.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.00, 1.00, 1.00 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.00 ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -1. : x_a = 0., y_a = 0., z_a = 1., c_a = 37.5000 : x_s = 0., y_s = -1., z_s = 0., c_s = 4.7185 talairach xfm : /pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 127. 0. 0. 1. -90.5000 0. -1. 0. 132.7185 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 127. -0. -0. -1. 132.7185 -0. 1. -0.90.5000 -0. -0. -0. 1. Is there any other way to resolve this issue than reconstruction the brain again and doing all the edits all over again hoping that the brain mask does not get corrupted this time? Appreciate any help with this. Best, Srishti ___ 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_vol2surf: unable to compare volume maps
Hi, I am trying to compare my volume maps (negative_allsocial_proportion.nii) to someone else's (SN_like_cortical_lh.nii.gz) who have it on a surface (mni152_subject). So I used the steps for mri_vol2surf command as follows: Commands: mri_vol2surf --src negative_allsocial_proportion.nii --regheader mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 Then to view it: tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 Everything ran fine and we didn't get any error but then while viewing the files we could not see our map (neg_allsocail_lh.nii) on the surface. This file seemed to work fine as it is not an empty file when I checked the file size. However, when we view it using tksurfer it does not show up as a highlighted portion on the surface. The SN_like_cortical_lh.nii.gz file shows up just fine. Could someone please help me figure out what might have gone wrong here. Thanks so much! ___ 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] mir_vol2surface registration file error
Hi, I tried using bbregister to register my files with the following command: bbregister --mov negative_allsocial.nii --bold --s SN_like_cortical_lh.gz --init-rr --lta register.lta and this is the error I received: reading source './tmp.bbregister.173331/template.nii'... mri_robust_register.bin: only pass single frame MRI source ./tmp.bbregister.173331/template.nii. No such file or directory I would like to re-iterate my issue as that might be helpful. We have carried out a meta analysis and want to compare our meta analytic maps to someone's else's map. Our meta analytic map is negative_allsocial.vmp which we converted to a nifti using neuroelf and now have the negative_allsocial.nii. We want to see how someone else's map which is the SN_like_cortical_lh.gz (they said to view this on a subject file to which they gave us the link) compares to our map. We would also further want to see how our map compares to their volume map which is SN_like_subcortical.nii (these are in MNI152 volume space). We are using mri_vol2surf to view compare the two files. mri_vol2surf --src negative_allsocial_proportion.nii --src_type analyze --srcreg [REGISTRATION MATRIX] --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 And for the registration matrix I tried using bbregister as told my the freeSurfer help group. I can send the files as well if required and would highly appreciate some prompt help on this. Thanks so much! Best, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Fri, Mar 9, 2018 at 11:15 AM, Douglas Greve <dgr...@mgh.harvard.edu> wrote: > You create it with bbregister. See the multimodal integration tutorial > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview > > On 3/6/18 6:36 PM, srishti goel wrote: > > I am sorry but that is what I am unsure about it. I don't know how to > obtain a registration matrix or which registration matrix to use for this. > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > On Mon, Mar 5, 2018 at 3:24 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > > wrote: > >> Why did you remove the registration file? --srcreg below >> >> >> On 02/28/2018 04:13 PM, srishti goel wrote: >> > Hello, >> > >> > Thank you so much! I used the following command as you said and got an >> > error : must specify a source registration file or --regheader >> > >> > mri_vol2surf --src negative_allsocial_avgnull.nii --src_type analyze >> > --trgsubject fsaverage --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 >> > >> > >> > Best, >> > Srishti >> > Social/Clinical Research Specialist >> > Child Imaging Research and Life Experiences Lab >> > University of North Carolina at Chapel Hill >> > email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> >> > skype: srishti.goel12 >> > >> > >> > On Wed, Feb 28, 2018 at 10:13 AM, Douglas Greve >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> > >> > you need to add --trgsubject fsaverage to your mri_vol2surf >> > command line >> > >> > >> > On 2/27/18 12:23 PM, srishti goel wrote: >> >> Hello, >> >> >> >> We are trying to project a volume map onto a surface. Our network >> >> based volume map is a .vmp file and our surface is a nifti file. >> >> We were able to convert the volume maps from .vmp to nifti. >> >> Our volume map is: negative_allsocial_proportion.nii >> >> Our surface is: SN_like_cortical_lh.nii >> >> The output file is named: neg_allsocial.nii >> >> >> >> We are trying to use the following command to now project the >> >> volume map on surface and the issues we are facing are: >> >> 1) We are unsure of what the purpose of the registration file is >> >> and where in the mir_vol2surf command should we specify the surface >> >> 2) If it is a matrix for something related to the surface on >> >> which we want to project our volume then how should we go about >> >> obtaining the registration file appropriate for our comparison. >> >> >> >> _Command:_ >> >> mri_vol2surf --src negative_allsocial
Re: [Freesurfer] mir_vol2surface registration file error
I am sorry but that is what I am unsure about it. I don't know how to obtain a registration matrix or which registration matrix to use for this. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Mon, Mar 5, 2018 at 3:24 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > Why did you remove the registration file? --srcreg below > > > On 02/28/2018 04:13 PM, srishti goel wrote: > > Hello, > > > > Thank you so much! I used the following command as you said and got an > > error : must specify a source registration file or --regheader > > > > mri_vol2surf --src negative_allsocial_avgnull.nii --src_type analyze > > --trgsubject fsaverage --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 > > > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> > > skype: srishti.goel12 > > > > > > On Wed, Feb 28, 2018 at 10:13 AM, Douglas Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > you need to add --trgsubject fsaverage to your mri_vol2surf > > command line > > > > > > On 2/27/18 12:23 PM, srishti goel wrote: > >> Hello, > >> > >> We are trying to project a volume map onto a surface. Our network > >> based volume map is a .vmp file and our surface is a nifti file. > >> We were able to convert the volume maps from .vmp to nifti. > >> Our volume map is: negative_allsocial_proportion.nii > >> Our surface is: SN_like_cortical_lh.nii > >> The output file is named: neg_allsocial.nii > >> > >> We are trying to use the following command to now project the > >> volume map on surface and the issues we are facing are: > >> 1) We are unsure of what the purpose of the registration file is > >> and where in the mir_vol2surf command should we specify the surface > >> 2) If it is a matrix for something related to the surface on > >> which we want to project our volume then how should we go about > >> obtaining the registration file appropriate for our comparison. > >> > >> _Command:_ > >> mri_vol2surf --src negative_allsocial_proportion.nii --src_type > >> analyze --srcreg [REGISTRATION MATRIX] --hemi lh --o > >> ./neg_allsocial.nii --projfrac 0.5 > >> > >> _Then to project it:_ > >> tksurfer fsaverage lh inflated -ov neg_allsocail.nii > >> > >> > >> > >> ___ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <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 >
Re: [Freesurfer] mir_vol2surface registration file error
Hello, Thank you so much! I used the following command as you said and got an error : must specify a source registration file or --regheader mri_vol2surf --src negative_allsocial_avgnull.nii --src_type analyze --trgsubject fsaverage --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Wed, Feb 28, 2018 at 10:13 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > you need to add --trgsubject fsaverage to your mri_vol2surf command line > > On 2/27/18 12:23 PM, srishti goel wrote: > > Hello, > > We are trying to project a volume map onto a surface. Our network based > volume map is a .vmp file and our surface is a nifti file. We were able to > convert the volume maps from .vmp to nifti. > Our volume map is: negative_allsocial_proportion.nii > Our surface is: SN_like_cortical_lh.nii > The output file is named: neg_allsocial.nii > > We are trying to use the following command to now project the volume map > on surface and the issues we are facing are: > 1) We are unsure of what the purpose of the registration file is and where > in the mir_vol2surf command should we specify the surface > 2) If it is a matrix for something related to the surface on which we want > to project our volume then how should we go about obtaining the > registration file appropriate for our comparison. > > *Command:* > mri_vol2surf --src negative_allsocial_proportion.nii --src_type analyze > --srcreg [REGISTRATION MATRIX] --hemi lh --o ./neg_allsocial.nii --projfrac > 0.5 > > *Then to project it:* > tksurfer fsaverage lh inflated -ov neg_allsocail.nii > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mir_vol2surface registration file error
Hello, We are trying to project a volume map onto a surface. Our network based volume map is a .vmp file and our surface is a nifti file. We were able to convert the volume maps from .vmp to nifti. Our volume map is: negative_allsocial_proportion.nii Our surface is: SN_like_cortical_lh.nii The output file is named: neg_allsocial.nii We are trying to use the following command to now project the volume map on surface and the issues we are facing are: 1) We are unsure of what the purpose of the registration file is and where in the mir_vol2surf command should we specify the surface 2) If it is a matrix for something related to the surface on which we want to project our volume then how should we go about obtaining the registration file appropriate for our comparison. *Command:* mri_vol2surf --src negative_allsocial_proportion.nii --src_type analyze --srcreg [REGISTRATION MATRIX] --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 *Then to project it:* tksurfer fsaverage lh inflated -ov neg_allsocail.nii ___ 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.
