Re: [Freesurfer] shift to account for hemodynamic response
Thank you so much. On Fri, Feb 9, 2018 at 11:48 AM, Douglas Greve wrote: > It is already built into the HRF model. If you need to shift them more or > less than what is in the model, that can be accommodated. If you use the > -spmhrf option, then you will get the same HRF as is used in spm. > > On 2/6/18 11:45 PM, Ashley Cole wrote: > > Dear experts, > > I just have switched from SPM to Freesurfer. I am wondering if in FSFAST > analysis, we require to shift the regressors in time to account for the > delay in hemodynamic response? > > Thanks > > > ___ > 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] V1 functional ROI
Dear Dr. Douge, I am a little bit confused about creating function ROI in V1. Basically, I have some localizers that for some ROIs I need to find activated neurons in a specific contrast in native space and then create that ROI and map it to my experimental scans and extract their voxel data. I have used this command for right-FFA: funcroi-config -seg aparc+aseg.mgz 2007 -analysis eba-fba.native.rh -c faces-vs-objects -thresh 3 -sign pos -roi rh.surface.pSTS.faces-vs-objects.thr3.pos.roicfg -force But now, for V1 I am not sure what should I use. Is this correct? funcroi-config -seg aparc+aseg.mgz 400 -analysis eba-fba.native.rh -c faces-vs-objects -thresh 3 -sign pos -roi rh.surface.V1.faces-vs-objects.thr3.pos.roicfg -force I don't see a number in the lookup table for left and right V1. On the other hand, there are V1 labels in the label folder. I appreciate your help. 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.
[Freesurfer] FIR analysis
Hi experts, I was wondering if there is any tutorial or example on FIR analysis. I don't know where to start. I need to look at the time course of some voxels. I have a localizer session and the main experiment. I am intending to find the ROIs in the localizer scans and then extract their time course activation in the main experiment scans. I have done the recon-all successfully. Then in my localizer scan, I did preproc-sess, mkanalysis-sess with FIR 6 24 flag, mkcontarst, and selxabg3. Now, I am lost. Sorry for my naiive question. Thank you, --SC ___ 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] Percent Signal Change
Hi, Could someone please let me know how to get the percent signal change for raw signal intensity? I think the cespct.nii.gz gives me the contrast as %. However, I am not sure about dividing h.nii and h-offset.nii. What are they? Thank you ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Percent Signal Change
Thank you, Doug. Sorry for not being clear. Could you please tell me what h.nii.gz and h-offset.nii.gz are? Also, do you have any recommendation on how to get % signal change on the signal intensity as oppose to % signal change on contrasts? Thank you On Thu, Feb 15, 2018 at 12:47 PM, Douglas N Greve wrote: > It divides the contast (ces) by voxel-wise mean. I'm not sure I > understand your quesstion about h and h-offset > > > On 02/15/2018 01:04 PM, Sarah Cole wrote: > > Hi, > > > > Could someone please let me know how to get the percent signal change > > for raw signal intensity? > > > > I think the cespct.nii.gz gives me the contrast as %. However, I am > > not sure about dividing h.nii and h-offset.nii. What are they? > > > > > > Thank you > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Percent Signal Change
Yes, that's exactly what I am looking for. Raw waveform as a percent. On Thu, Feb 15, 2018 at 1:00 PM, Douglas N Greve wrote: > h-offset is the intensity offset (basically the mean signal). h.nii.gz > is a complicated combination of the betas (regression coefficients) that > is included for backwards compatibility. What do you mean by % signal > change? Do you want the raw waveform as a percent? > > > On 02/15/2018 01:52 PM, Sarah Cole wrote: > > Thank you, Doug. > > > > Sorry for not being clear. Could you please tell me what h.nii.gz and > > h-offset.nii.gz are? > > > > Also, do you have any recommendation on how to get % signal change on > > the signal intensity as oppose to % signal change on contrasts? > > > > Thank you > > > > On Thu, Feb 15, 2018 at 12:47 PM, Douglas N Greve > > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > It divides the contast (ces) by voxel-wise mean. I'm not sure I > > understand your quesstion about h and h-offset > > > > > > On 02/15/2018 01:04 PM, Sarah Cole wrote: > > > Hi, > > > > > > Could someone please let me know how to get the percent signal > > change > > > for raw signal intensity? > > > > > > I think the cespct.nii.gz gives me the contrast as %. However, I am > > > not sure about dividing h.nii and h-offset.nii. What are they? > > > > > > > > > Thank you > > > > > > > > > ___ > > > 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> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > ___ > > 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 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Goodness of fit
Hi Doug, I have used spmhrf 0 in my FS-FAST analysis. I was wondering if there is any way to check the variance explained and fits on the model? Thank you, -S ___ 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] Goodness of fit
Great. Thank you very much. On Tue, Feb 20, 2018 at 11:19 AM, Douglas N Greve wrote: > I don't output a variance explained per se. You can get p-values > (sig=-log10(p)) and partial correlation coefficient (pcc) for a given > regressor or contrast > > > On 02/20/2018 12:07 PM, Sarah Cole wrote: > > Hi Doug, > > > > > > I have used spmhrf 0 in my FS-FAST analysis. I was wondering if there > > is any way to check the variance explained and fits on the model? > > > > > > Thank you, > > > > -S > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Creating ROI on the functional map
Hi, I was wondering if this method is still applicable in version 6 https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs I cannot seem to find any of the options for creating an ROI. Thank you, S ___ 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] Creating ROI on the functional map
It doesn't work on tksurfer. But it's ok. So Doug, is this the latest tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview for FS-FAST and creating functional ROI? More specifically, do I need to use "mri_vol2surf" to get the activation on the surface? This was not in the other tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastFirstLevel Thanks On Mon, Feb 26, 2018 at 3:28 PM, Douglas N Greve wrote: > I think it should work; We are not using tksurfer any more (freeview > instead), but I think it should still work > > > On 02/23/2018 05:16 PM, Sarah Cole wrote: > > Hi, > > > > I was wondering if this method is still applicable in version 6 > > https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs > > > > > > I cannot seem to find any of the options for creating an ROI. > > > > Thank you, > > > > S > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Creating ROI on the functional map
I apologize. I was wrong. Thanks, S On Mon, Feb 26, 2018 at 5:16 PM, Sarah Cole wrote: > It doesn't work on tksurfer. But it's ok. > > So Doug, is this the latest tutorial: https://surfer.nmr.mgh. > harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview for > FS-FAST and creating functional ROI? > > More specifically, do I need to use "mri_vol2surf" to get the activation > on the surface? > > This was not in the other tutorial: http://surfer.nmr.mgh.harvard. > edu/fswiki/FsFastTutorialV6.0/FsFastFirstLevel > > > Thanks > > On Mon, Feb 26, 2018 at 3:28 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> I think it should work; We are not using tksurfer any more (freeview >> instead), but I think it should still work >> >> >> On 02/23/2018 05:16 PM, Sarah Cole wrote: >> > Hi, >> > >> > I was wondering if this method is still applicable in version 6 >> > https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs >> > >> > >> > I cannot seem to find any of the options for creating an ROI. >> > >> > Thank you, >> > >> > S >> > >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Freeview update on Mac
Hi Doug/Zeke, Could you please update the page for freeview update on Mac- if it is available. https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Thanks, S ___ 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] Fwd: Freeview update on Mac
Great! Thank you so much, Andrew. I downloaded the updated Freeview. I am still wondering how to draw an ROI on the surface in Freeview. I don't have the options. Could you please let me know what command you are running to get the Freeview? I am having the updated version Jan 2018. Thanks, Sarah On Tue, Feb 27, 2018 at 11:40 AM, Hoopes, Andrew wrote: > Hi Sarah, I updated the wiki page. We actually just put up a standalone, > dev freeview app today. > > best > Andrew > > > On February 27, 2018 at 11:38:57 AM, Sarah Cole (coleashle...@gmail.com) > wrote: > > Hi Doug/Zeke, > > Could you please update the page for freeview update on Mac- if it is > available. > > https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview > > > Thanks, > > S > ___ > 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] Hemodynamic Lag Shift
Hi Doug, I have a block design experiment. After analyzing the data and plotting the response magnitude across the TRs, we see that there is a systematic lag in the response. For example, in a 16s block (TR=2s), at TR-1 and TR-2 the response goes down and then starts rising from TR-3. This is consistent across the subjects and blocks. We used to shift our raw data by 2 TRs when we were using SPM. How can we do this in FreeSurfer? Thank you, Sarah ___ 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] Hemodynamic Lag Shift
Thanks, Doug. I added (-4s) delay and plotted the data but I got the same delay as no shift. Also I did (+4) delay and lost most of the activation. Do you have any recommendations? Thanks, Sarah On Wed, Mar 28, 2018 at 4:39 PM, Douglas N. Greve wrote: > You can use the -delay flag in mkanalysis-sess > > doug > > > On 03/28/2018 05:35 PM, Sarah Cole wrote: > > Hi Doug, > > > > I have a block design experiment. After analyzing the data and > > plotting the response magnitude across the TRs, we see that there is a > > systematic lag in the response. For example, in a 16s block (TR=2s), > > at TR-1 and TR-2 the response goes down and then starts rising from > > TR-3. This is consistent across the subjects and blocks. > > > > We used to shift our raw data by 2 TRs when we were using SPM. > > > > How can we do this in FreeSurfer? > > > > Thank you, > > > > Sarah > > > > > > ___ > > 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] Hemodynamic Lag Shift
Hi Doug, Sure. I have attached an excel sheet. I have averaged the signal magnitude across 16 blocks of objects, and 16 blocks of scenes, separately. Each block has 8 TRs (TR=2). The top plot is the data with the default -TR/2 delay. The bottom plot is the data with -2TR delay. In both plots, we see that the signal drops in the first 2 TRs and then starts rising around TR 3. We would like to see this rise at TR1, that's why we think that we need to shift the onset times. However, when we added the -2TR delay, we still got the same fall and rise. This pattern is consistent across all subjects. When we were using SPM, we always shifted the signal by 2TRs and always saw the rise at the first TR. I am not sure what I am doing wrong, here. Appreciate your help. Thanks, On Fri, Mar 30, 2018 at 8:09 AM, Douglas Greve wrote: > not sure what you are trying to do. can you send a picture? the default > lag is TR/2 > > On 3/29/18 2:30 PM, Sarah Cole wrote: > > Thanks, Doug. > > I added (-4s) delay and plotted the data but I got the same delay as no > shift. Also I did (+4) delay and lost most of the activation. > > Do you have any recommendations? > > Thanks, > Sarah > > On Wed, Mar 28, 2018 at 4:39 PM, Douglas N. Greve > wrote: > >> You can use the -delay flag in mkanalysis-sess >> >> doug >> >> >> On 03/28/2018 05:35 PM, Sarah Cole wrote: >> > Hi Doug, >> > >> > I have a block design experiment. After analyzing the data and >> > plotting the response magnitude across the TRs, we see that there is a >> > systematic lag in the response. For example, in a 16s block (TR=2s), >> > at TR-1 and TR-2 the response goes down and then starts rising from >> > TR-3. This is consistent across the subjects and blocks. >> > >> > We used to shift our raw data by 2 TRs when we were using SPM. >> > >> > How can we do this in FreeSurfer? >> > >> > Thank you, >> > >> > Sarah >> > >> > >> > ___ >> > 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 > 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. > > HRF_Shift_FSFAST.xlsx Description: MS-Excel 2007 spreadsheet ___ 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] Hemodynamic Lag Shift
Please ignore my previous post. I was wrong on so many levels! Thanks S On Fri, Mar 30, 2018 at 8:34 AM, Sarah Cole wrote: > Hi Doug, > > Sure. I have attached an excel sheet. > I have averaged the signal magnitude across 16 blocks of objects, and 16 > blocks of scenes, separately. Each block has 8 TRs (TR=2). > > The top plot is the data with the default -TR/2 delay. > The bottom plot is the data with -2TR delay. > > In both plots, we see that the signal drops in the first 2 TRs and then > starts rising around TR 3. We would like to see this rise at TR1, that's > why we think that we need to shift the onset times. > However, when we added the -2TR delay, we still got the same fall and > rise. This pattern is consistent across all subjects. > > When we were using SPM, we always shifted the signal by 2TRs and always > saw the rise at the first TR. I am not sure what I am doing wrong, here. > > Appreciate your help. > > Thanks, > > On Fri, Mar 30, 2018 at 8:09 AM, Douglas Greve > wrote: > >> not sure what you are trying to do. can you send a picture? the default >> lag is TR/2 >> >> On 3/29/18 2:30 PM, Sarah Cole wrote: >> >> Thanks, Doug. >> >> I added (-4s) delay and plotted the data but I got the same delay as no >> shift. Also I did (+4) delay and lost most of the activation. >> >> Do you have any recommendations? >> >> Thanks, >> Sarah >> >> On Wed, Mar 28, 2018 at 4:39 PM, Douglas N. Greve > > wrote: >> >>> You can use the -delay flag in mkanalysis-sess >>> >>> doug >>> >>> >>> On 03/28/2018 05:35 PM, Sarah Cole wrote: >>> > Hi Doug, >>> > >>> > I have a block design experiment. After analyzing the data and >>> > plotting the response magnitude across the TRs, we see that there is a >>> > systematic lag in the response. For example, in a 16s block (TR=2s), >>> > at TR-1 and TR-2 the response goes down and then starts rising from >>> > TR-3. This is consistent across the subjects and blocks. >>> > >>> > We used to shift our raw data by 2 TRs when we were using SPM. >>> > >>> > How can we do this in FreeSurfer? >>> > >>> > Thank you, >>> > >>> > Sarah >>> > >>> > >>> > ___ >>> > 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 >> 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.
Re: [Freesurfer] Percent Signal Change
Doug,
Could you please let me know what this line is doing?
"fmnrep = repmat(fmn,[1 1 1 size(f.vol,3)]);"
When I try to assign f.vol/fmnrep to s.vol (this line s.vol =
f.vol./fmnrep;), matrices do not match in dimension.
Thanks,
S
On Thu, Feb 15, 2018 at 1:05 PM, Douglas N Greve
wrote:
> That does not get computed. You can do it in matlab with something like
>
> f = MRIread('f.nii.gz');
>
> fmn = mean(f.vol,4);
>
> fmnrep = repmat(fmn,[1 1 1 size(f.vol,3)]);;
>
> s = f;
>
> s.vol = f.vol./fmnrep;
>
> MRIwrite(s,'percentchange.nii.gz')
>
>
>
> On 02/15/2018 02:03 PM, Sarah Cole wrote:
> > Yes, that's exactly what I am looking for. Raw waveform as a percent.
> >
> > On Thu, Feb 15, 2018 at 1:00 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > h-offset is the intensity offset (basically the mean signal).
> h.nii.gz
> > is a complicated combination of the betas (regression
> > coefficients) that
> > is included for backwards compatibility. What do you mean by % signal
> > change? Do you want the raw waveform as a percent?
> >
> >
> > On 02/15/2018 01:52 PM, Sarah Cole wrote:
> > > Thank you, Doug.
> > >
> > > Sorry for not being clear. Could you please tell me what
> > h.nii.gz and
> > > h-offset.nii.gz are?
> > >
> > > Also, do you have any recommendation on how to get % signal
> > change on
> > > the signal intensity as oppose to % signal change on contrasts?
> > >
> > > Thank you
> > >
> > > On Thu, Feb 15, 2018 at 12:47 PM, Douglas N Greve
> > > mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> > >
> > > It divides the contast (ces) by voxel-wise mean. I'm not sure I
> > > understand your quesstion about h and h-offset
> > >
> > >
> > > On 02/15/2018 01:04 PM, Sarah Cole wrote:
> > > > Hi,
> > > >
> > > > Could someone please let me know how to get the percent
> signal
> > > change
> > > > for raw signal intensity?
> > > >
> > > > I think the cespct.nii.gz gives me the contrast as %.
> > However, I am
> > > > not sure about dividing h.nii and h-offset.nii. What are
> they?
> > > >
> > > >
> > > > Thank you
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu
> >>
> > > Phone Number: 617-724-2358
> > >
> > > Fax: 617-726-7422 > >
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > > <https://gate.nmr.mgh.harvard.edu/filedrop2
> > <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> &
[Freesurfer] Canonical HRF shape generated by FSFAST
Hi Doug, At the end of my FSFAST analysis, I would like to plot the Canonical HRF shape generated by FSFAST for my events. I have found this thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-July/031902.html but I am not sure if I understand this line: "plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf)" Could you please clarify how to plot the Canonical HRF that was generated by FSFAST? Thank you, Sarah ___ 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] Canonical HRF shape generated by FSFAST
Just one clarification, this is for first level analysis (individual subjects). Thanks On Wed, Apr 11, 2018 at 9:54 AM, Sarah Cole wrote: > Hi Doug, > > At the end of my FSFAST analysis, I would like to plot the Canonical HRF > shape generated by FSFAST for my events. I have found this thread: > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013- > July/031902.html > > but I am not sure if I understand this line: " > plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf)" > > > Could you please clarify how to plot the Canonical HRF that was generated > by FSFAST? > > Thank you, > > Sarah > ___ 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] FSFAST, Beta values and Percent Signal Change questions
Hi Doug, I need your recommendations on two topics. I really appreciate your help. 1.) I have two runs of the same experiment, each for about 12 minutes. These 2 runs are different only in the presentation order of the stimuli. I also have one localizer session which first, I calculated my contrasts in it, found the active voxels with positive values, and made a mask of those voxels. Then, mapped the masks on those 2 runs and got the raw data within those voxels. So far, so good. Now, I am looking at the Beta values in these 2 runs for those active voxels, they are very different from each other. For example, in the first run, they are mostly positive but in the second run, they are mostly negative. My intuition was that they should be in the same ballpark. I cannot make sense of this. Do you have any suggestions on why this is happening? 2.) To calculate the % signal change, is it ok to pick the baseline whatever is suitable to my research question. For example, if I need to know the % signal change relative to* the average signal in the first TR of a specific block*, can I use that as a baseline? Or does it always need to be the rest or the mean? Thank you so much and looking forward to hearing from you. Sarah ___ 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] key nSliceGroups unrecognized, line 11, skipping
External Email - Use Caution Hi, I know this is not an error but just a comment. But may I know what this means: "*key nSliceGroups unrecognized, line 11, skipping"* I tried to look for line 11 in matlab scripts but they are mainly commented out. Thank you, Sara ___ 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.
