Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

bring volumes to fsaverage space
by Shani Ben Amitay 04 Dec '15

04 Dec '15

Dear freesurfers, I would like to know what will be the best way to bring volumes in the individual subject's space to the fsaverage space. Thanks, Shani

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converting labels to MNI space
by Francesca Strappini 03 Dec '15

03 Dec '15

Dear FreeSurfer experts, I'm trying to convert some retinotopic labels I created on the surface of each individual subject to MNI305 space for FSL. I run the following commands, but the output is not registered correctly. It seems to be shifted downward. mni152reg --s LG mri_label2label --srclabel lh.V1dorsalLG.label --s LG --regmethod surface --trglabel lh.V1dorsalLG_new.label --hemi lh mri_label2vol --label lh.V1dorsalLG_new.label --reg /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o lh.V1dorsalLG_new_MNI.nii.gz Thanks for your help, Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image
by Ajay Kurani 03 Dec '15

03 Dec '15

Hello Freesurfer experts, I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version) with the -hires flag to process an MNI template image which is 0.5mm isotropic. Stage 1 ran well and on stage 2 there is an error during pocessing: Command run: recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts I supplied a skull stripped brain which was nu corrected and so I used the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 stage. I then ran autorecon2 and it was working well until I was at the -fix stage and ran into the following error: Error: mris_euler_number ./surf/lh.orig mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list I am not sure if this is due to the fact that we have a very high resolution image (template) and if there are any modifications needed aside from the hires flag. Are there any suggestions you have? Thanks, Ajay

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White matter and cp edits don't produce new results after reconall
by Annelinde Vandenbroucke 02 Dec '15

02 Dec '15

Dear all, I have a faulty wm map (brainmask.mgz) where some regions are not labeled as white matter where they should. I tried to correct both the wm.mgz map and add control points (and saved these), afterwards running either -autorecon2-wm or autorecon2-cp, but neither of these work. I can see the control points and wm edits in my maps, but the wm segmentation is still the same. I have not found a solution on the mailing list yet and was wondering whether anybody had a similar problem or could help. Thank you in advance, Annelinde -- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720

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Freesurfer Regions
by Ananth Narayanan 02 Dec '15

02 Dec '15

Hello freesurfer users, I am a new user of freesurfer. We are using FS to define ROIs for out PET analysis. I looked at the FS color lookup table, and saw the following ROIs. 8001 Thalamus-Anterior 74 130 181 0 8002 Thalamus-Ventral-anterior 242 241 240 0 8003 Thalamus-Lateral-dorsal 206 65 78 0 8004 Thalamus-Lateral-posterior 120 21 133 0 8005 Thalamus-Ventral-lateral 195 61 246 0 8006 Thalamus-Ventral-posterior-medial 3 147 6 0 8007 Thalamus-Ventral-posterior-lateral 220 251 163 0 8008 Thalamus-intralaminar 232 146 33 0 8009 Thalamus-centromedian 4 114 14 0 8010 Thalamus-mediodorsal 121 184 220 0 8011 Thalamus-medial 235 11 175 0 8012 Thalamus-pulvinar 12 46 250 0 8013 Thalamus-lateral-geniculate 203 182 143 0 8014 Thalamus-medial-geniculate 42 204 167 0 Where can I find these regions? 9000 ctx-lh-prefrontal 30 5 30 0 9001 ctx-lh-primary-motor 30 100 45 0 9002 ctx-lh-premotor 130 100 165 0 9003 ctx-lh-temporal 105 25 5 0 9004 ctx-lh-posterior-parietal 125 70 55 0 9005 ctx-lh-prim-sec-somatosensory 225 20 105 0 9006 ctx-lh-occipital 225 20 15 0 9500 ctx-rh-prefrontal 30 55 30 0 9501 ctx-rh-primary-motor 30 150 45 0 9502 ctx-rh-premotor 130 150 165 0 9503 ctx-rh-temporal 105 75 5 0 9504 ctx-rh-posterior-parietal 125 120 55 0 9505 ctx-rh-prim-sec-somatosensory 225 70 105 0 9506 ctx-rh-occipital 225 70 15 0 Also, where can I find functionally defined regions of interest? I noticed the above in the FS lookup table as well. Like the dlPFC (bilateral) and the SM1 regions of interest? But again, I can't find it. Thank you. 'Sincerely, - Ananth

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Sign option of Monte Carlo simulation in QDEC
by Karl Liu 01 Dec '15

01 Dec '15

Dear experts: In examining QDEC results of a contrast of interest, I noticed the results are mainly in cold color (blue), with only two small clusters in warm color (red). When I proceeded with Monte Carlo simulation, if I chose the abs as the sign option in simulation, then no clusters survived. In contrast, some clusters would remain, if I chose the neg sign. Because the uncorrected results were mainly in cold color, it seems reasonable to me to use negative only in the simulation. But I am wondering how the option of abs/neg/pos leads to the disparities and will you please elaborate how the simulation works based on abs/neg/pos. Thank you in advance. Karl

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Still unsure how to create my 3g4v matrix
by nellie 01 Dec '15

01 Dec '15

Hi expert, Thank you for your reply. I had read the example tables, but I'm still not sure how to alter them into my analysis.Can you help me to check the matrix I designed and point out my mistakes? Thanks in advence. 3 classes ( A / B / C group) and 4 variables (gender, age, education, and Moca test score). group.diff.mtx 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 group-x-gender.mtx 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 group-x-age.mtx 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 group-x-education.mtx 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 group-x-moca.mtx 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 group-x-gender-x-age-x-education.mtx 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 group-x-gender-x-age-x-education-x-moca.mtx 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 group.diff.mtx also can write as: 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 group-x-age.mtx aslo can write as: 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 . Wishes, Li > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Freesurfer digest..." > > >Today's Topics: > > 1. Re: How to create a 3g4v matrix (Lee Tirrell) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Mon, 23 Nov 2015 10:27:42 -0500 (EST) >From: Lee Tirrell <ltirrell(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] How to create a 3g4v matrix >To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >Message-ID: > <alpine.LRH.2.20.1511231020130.5623(a)vermis.nmr.mgh.harvard.edu> >Content-Type: text/plain; charset="iso-8859-7" > >Hi Li, > >You can find some example FSGD tables here, which you can alter to fit your >analyses. > >https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > >Best, >Lee > >On Sun, 22 Nov 2015, nellie wrote: > >> >> Hi Freesurfer Experts, >> >> I?m a new user of Freesurfer, and I learn how to use this software mainly through Wiki. When I came to the step of using GLM to compare group differences, I was confused on the design of 3g4v matrix. In my study, there were 3 classes ( >> A / B / C group) and 4 concomitant?variables (gender, age, education, and Moca test score). It?s supposed to be 15 regressors in this design, but I don?t know how to use the numbers (like 1, -1, 0, 0.5, -0.5, etc.) to create a correct >> matrix. I wonder if you could provide a 3g4v matrix in detail for me. I?ll be grateful if you can help. I hope I?m not bothering you too much, and I?m looking for your reply. >> >> Best wishes, >> >> Li? >> >> >> >> ? >> >> >> > >------------------------------ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >End of Freesurfer Digest, Vol 141, Issue 40 >******************************************* > > >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. >

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Create surface overlay from p-values
by Bronwyn Overs 30 Nov '15

30 Nov '15

Hi Freesurfer mailing list, Using an external software package we have completed of analysis for the vtx-wise thickness data extracted from freesurfer. We now have a p-value array containing one value for each vtx, and we would like to map this back onto the brain surface. Is there a way to create a .mgh overlay from our array of p-values using fsaverage as the subject? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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FSGD File Formatting Error
by Shady El Damaty 30 Nov '15

30 Nov '15

Hi Freesurfers, I'm having some issues running mri_glmfit using a simple custom GLM file. I've double checked to make sure the subject session file passed to isxconcat-sess is the same as the fsgd file and also checked the formatting corresponds with what is posted online however I keep getting the same error: ERROR: gdfReadV1: Input line 1, subjid = A02217-w2 Found 43 variables, expected. 1 FSGDF Format Error: file = /Users/seldamat/Dropbox/Projects/ADS/data/ads.emostroop.marketing/new.exposure.fsgd, tag=Input ERROR: cannot find glm-exposure My fsgd file is attached. Please any help would be greatly appreciated on this time sensitive matter. Thank you, Shady On Thu, Nov 26, 2015 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. voxel value scaling (Rockers, Elijah D.) > 2. Re: voxel value scaling (Douglas Greve) > 3. Re: voxel value scaling (Rockers, Elijah D.) > 4. Re: Error - extracting percent signal (Douglas Greve) > 5. Re: bring volumes to fsaverage space (Andrew Bock) > 6. FS v.6.0 (Th?c Trinh) > 7. recon-all with more than 10 inputs (???) > 8. Re: Multiple comparisons to confirm atrophy (Anderson M. Winkler) > 9. report a bug (salvatoreandrea.92(a)libero.it) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 25 Nov 2015 17:08:28 +0000 > From: "Rockers, Elijah D." <edrockers(a)houstonmethodist.org> > Subject: [Freesurfer] voxel value scaling > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <5655EB0C.1000309(a)houstonmethodist.org> > Content-Type: text/plain; charset="utf-8" > > I am interested in finding a way to apply a slope scaling factor to the > voxel values in a NIfTI image. > > I have done this in MATLAB and PMOD so far, but for some reason both > methods change the origin or otherwise distort the dimensions of the > image and render it impossible for me to process further. > > Something that simply scales the values without touching the header (or > at least as little as possible) would be great. Is anything like this > out there? > > Thanks, > > Eli > > Houston Methodist. Leading Medicine. > > Ranked by U.S.News & World Report as one of America's "Best Hospitals" in > 11 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work > For?" list 10 years in a row. Designated as a Magnet hospital for > excellence in nursing. Visit us at houstonmethodist.org. Follow us at > twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston > Methodist Hospital and/or its relevant affiliates and may contain > restricted and privileged material for the sole use of the intended > recipient(s). Any review, use, distribution or disclosure by others is > strictly prohibited. If you are not the intended recipient (or authorized > to receive for the recipient), please contact the sender and delete all > copies of the message. Thank you. > > > > ------------------------------ > > Message: 2 > Date: Wed, 25 Nov 2015 12:54:23 -0500 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] voxel value scaling > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <5655F5CF.8050907(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > You can use fscalc, something like > fscalc input.nii mul 10 -o output.nii > I think you can use fslmaths as well > > On 11/25/15 12:08 PM, Rockers, Elijah D. wrote: > > I am interested in finding a way to apply a slope scaling factor to the > > voxel values in a NIfTI image. > > > > I have done this in MATLAB and PMOD so far, but for some reason both > > methods change the origin or otherwise distort the dimensions of the > > image and render it impossible for me to process further. > > > > Something that simply scales the values without touching the header (or > > at least as little as possible) would be great. Is anything like this > > out there? > > > > Thanks, > > > > Eli > > > > Houston Methodist. Leading Medicine. > > > > Ranked by U.S.News & World Report as one of America's "Best Hospitals" > in 11 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work > For?" list 10 years in a row. Designated as a Magnet hospital for > excellence in nursing. Visit us at houstonmethodist.org. Follow us at > twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. > > > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston > Methodist Hospital and/or its relevant affiliates and may contain > restricted and privileged material for the sole use of the intended > recipient(s). Any review, use, distribution or disclosure by others is > strictly prohibited. If you are not the intended recipient (or authorized > to receive for the recipient), please contact the sender and delete all > copies of the message. Thank you. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 25 Nov 2015 18:01:37 +0000 > From: "Rockers, Elijah D." <edrockers(a)houstonmethodist.org> > Subject: Re: [Freesurfer] voxel value scaling > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Cc: "Pascual, Maria B." <BPascual(a)houstonmethodist.org>, "Xue, Zhong" > <ZXue(a)houstonmethodist.org> > Message-ID: <5655F781.6000609(a)houstonmethodist.org> > Content-Type: text/plain; charset="utf-8" > > Great thank you! > > On 11/25/2015 11:54 AM, Douglas Greve wrote: > > You can use fscalc, something like > > fscalc input.nii mul 10 -o output.nii > > I think you can use fslmaths as well > > > > On 11/25/15 12:08 PM, Rockers, Elijah D. wrote: > >> I am interested in finding a way to apply a slope scaling factor to the > >> voxel values in a NIfTI image. > >> > >> I have done this in MATLAB and PMOD so far, but for some reason both > >> methods change the origin or otherwise distort the dimensions of the > >> image and render it impossible for me to process further. > >> > >> Something that simply scales the values without touching the header (or > >> at least as little as possible) would be great. Is anything like this > >> out there? > >> > >> Thanks, > >> > >> Eli > >> > >> Houston Methodist. Leading Medicine. > >> > >> Ranked by U.S.News & World Report as one of America's "Best Hospitals" > in 11 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work > For?" list 10 years in a row. Designated as a Magnet hospital for > excellence in nursing. Visit us at houstonmethodist.org. Follow us at > https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHo… > and > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.facebook.com_Housto… > . > >> > >> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston > Methodist Hospital and/or its relevant affiliates and may contain > restricted and privileged material for the sole use of the intended > recipient(s). Any review, use, distribution or disclosure by others is > strictly prohibited. If you are not the intended recipient (or authorized > to receive for the recipient), please contact the sender and delete all > copies of the message. Thank you. > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > > > > > > 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 > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… > . 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. > > > > ------------------------------ > > Message: 4 > Date: Wed, 25 Nov 2015 13:03:39 -0500 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Error - extracting percent signal > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <5655F7FB.8010801(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > It looks like the ces input is from a surface-based analysis. If you're > label is already on the surface, then no need to do the label2vol step. > If it is in the volume, then you'll need to transfer it to the surface > with mri_label2label with the --paint option > doug > > On 11/24/15 12:14 PM, Danielle Miller wrote: > > Hello freesurfer experts, > > > > I am trying to extract an average percent signal change from a > > functional roi label I created in tkmedit using fsaverage. I followed > > previously discussed methods: > > > > 1) mri_label2vol --label <name of label> --temp > > fsaverage/mri.2mm/orig.mgz --regheader fsaverage/mri/orig.mgz --o > > <name of label mask> > > > > 2) I checked (tkmedit fsaverage orig.mgz -overlay <label mask> > > -fminmax .5 1) and the label looked fine > > > > 3) I ran mri_segstats --i ces.nii.gz --seg <label mask from above> > > --id 1 --avgwf ces.label.dat > > ces.nii.gz is the file from my group analysis (isxconcat-sess) using > > the correct contrast > > It returns with this error: > > ERROR: dimension mismatch between input volume and seg > > input 163842 1 1 > > seg 76 76 93 > > > > Is there something I am doing wrong here? > > > > Also of note I tried using the following commands: > > 1) funcroi-config -label <label mask created from above mri_label2vol> > > -analysis <analysis directory> -roi <name of roicfg file> > > > > 2) funcroi-sess -sf sessid - roi <roicfg file from above> > > But this returns with this error: > > ERROR: cannot find > > > /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_001_recon/label/label_lh_ACC_correct_mask.mgz > > > > > > Any suggestions would be extremely helpful. > > > > Thanks, > > Danielle > > -- > > Ph.D. Program in Behavioral Neuroscience > > Boston University School of Medicine L-815 > > 72 E. Concord St > > Boston, MA 02118 > > > > > > VA Boston Healthcare System Jamaica Plain > > Memory Disorders Research Center > > 150 South Huntington Ave D11-103 > > Boston, MA 02130 > > OFFICE:(857) 364-2130 > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Re: [Freesurfer] Freesurfer Digest, Vol 141, Issue 48
by Bishesh Khanal 30 Nov '15

30 Nov '15

> Message: 14 > Date: Mon, 30 Nov 2015 09:32:54 -0500 > From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] long run fails for new time-point when > removing a tpt that was added with -addtp option > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <565C5E16.3060301(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi Bishesh, > > Disclaimer up front: > You probably know that adding time points without re-creating the base > is dangerous (as you bias you analysis, because not all time points are > treated the same). > > Thanks Martin. Yes I understand that but I'm trying to use recon-all in a different setting. For e.g. if I want to compare FreeSurfer results on repeat scans: new1 and new2 both taken on the same day, I understand that ideally one would do two different long runs by including new1 and new2 separately during the creation of base template and then compare the results. However, in my case instead of just new1 and new2, I have several of them that are simulated using different methods and these simulated images will be very close to the images that were already used during the base template creation. So I did not want to recreate the base template for each of these several cases. I want to analyse results on these new1, new2, new3, ..., newN simulated scans of the "same time-point" image but with different methods without recreating the base-template and providing the identical scenario for each of these new1, new2, ..., newN images in long-run. > Now here is why you see the error. > The way a new time points get added to an existing base is this: > 1. register the new time point's norm.mgz to the base norm.mgz (using > mri_robust_register and creates the lta files in mri/transforms) > 2. create a new temporary base norm.mgz from all time points and diff > with existing base norm.mgz > 3. report difference (the idea is to decide if the difference is small > then everything is fine and if it is large, recommend to re-run the base > from scratch, this is not implemented yet and you only see output and it > will always go through) > 4. add the new time point id to the list in base/base-tps > > So for step 3 it needs the norm.mgz from all other time points, to > re-create a temporary norm in the base. > > Now, how can you achieve what you want. I can think of two options: > - edit the base-tps and remove the line with new1 > this should work, the additional transforms to and from new1 (in > base/mri/transforms) can be left behind as they will not be used (you > can also delete those if you like) > - create two copies of the original base (before adding any time > points), then add each time point to each of the two copies. This is > absolutely safe as you make sure that new1 does not affect anything when > adding new2. > Yes if I had only two tpts, copying could be reasonable too, but I have few more, so I'm now considering the first option. Or a quicker way for me could be to temporarily comment out steps 2 and 3 you mentioned above. Could you tell me where in recon-all I could do that ? Thanks, Bishesh > > Anyway, I don't see why anyone would want to do what you are trying to > do, but good luck. > > Best, Martin > > On 11/30/2015 05:53 AM, Bishesh Khanal wrote: > > Hello, > > I had run a longitudinal run by creating a base template with a set of > > time-point scans (tpts). I wanted to add a new tpt (say new1) without > > recreating the base template, hence I used the option -addtp in the > > recon-all -long run. Later on, I no longer needed the results of the > > long run for new1. So I removed the relevant directories for new1 > > (i.e. new1 and new1.long.baseid). > > > > Now I have another tpt (say new2) for which I want a -long run without > > recreating the base template. So I did the same thing as before i.e. > > first a cross run for new2 (which worked fine) and then a long-run > > with -addtp option. However, the long-run for new2 failed with an > > error that it cannot find $SUBJECTS_DIR/new1/mri/norm.mgz > > > > I realize that although I had removed the relevant directories of > > new1, it is still listed in the file $SUBJECTS_DIR/baseid/base-tps. > > However, I do not understand why norm.mgz of new1 is needed by > > recon-all for a long run on new2 when I did not want FreeSurfer to use > > either of new1 or new2 to recreate the base. Ideally, I would want to > > run long run on new1 and new2 under identical conditions. In other > > words, I do not want long-run on new2 tpt to require results from long > > run on new1 tpt. Should it not be the expected behaviour when I am not > > using new1 and/or new2 to create the base template ? > > And, is there a way to do achieve what I want to without manually > > deleting the new1 from the list in the file > > $SUBJECTS_DIR/baseid/base-tps ? > > > > P.S. Initially, the -addtp option had not worked and I had to do the > > following to make it work: > > > > The FreeSurfer version: 5.3.0. Getting around a know bug. in recon-all > > in the following block (around line 6148) > > > > if ( ! $found_tpNid ) then > > echo "ERROR: $tpNid is not in > > ${longbasedir}/${BaseSubjsListFname}" > > echo "" > > exit 1 > > endif > > > > > > replaced the first line (if statement) with: > > > > if ( ! $found_tpNid && ! $DoAddTp ) then > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu > >

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Freesurfer November 2015